The Link
by Anjirika
Summary: –1st sparky story– When searching Atlantis both John and Elizabeth are exposed to Ancient technology. They are linked together and while dealing with their new ability they have to deal with the ramifications as problems descend on the city. R
1. The Link

Disclaimer: None of these characters are mine, I wish they were, but they aren't. This story is has Sparky undertones…..ok Sparky overtones- but if they could do it for Long Goodbye then I can do it for this!

* * *

Stargate Atlantis- Sometime in season 3, perhaps the end of the season, maybe a cliff hanger.

A/N: ('thoughts') ("dialogue") ( scene changes). Enjoy!

**The Link**

**Part 1**

Rodney McKay and John Sheppard were walking down a deserted hallway in the north pier of the ancient city of Atlantis. Rodney was clearly fascinated in the ancient device, referring to it and then looking around to the dimly lit, damp hallway while John was getting more and more bored.

"So, how much longer?" Colonel John Sheppard asked pulling his P-90 up to his chest looking to Rodney.

"Sheppard I have no idea." Rodney replied with frustration in his voice. "This power source is extremely weak and it is hard to pin down."

"And yet," John countered with frustration in his voice as well, "you saw it in the ancient main-frame."

"Well," Rodney began stopping in the hallway, "even a faint power source coming from the north pier- which I might add- hasn't been checked out fully yet and we've been here for what, two years now and still nothing and-"

"Your point Rodney?" John interrupted.

"What? Oh yes, well, the power source might be faint but it alerted us that something was in this general vicinity because it has always been shut down." Rodney explained starting to walk again.

"Even with the ZPM powering the city?" John asked following.

"Yes Sheppard." Rodney stated with exasperation. "Even with a ZedPM powering the city, it has been shut down."

"Now, why is that again?" John asked, his frustration leaving and enjoyment of tormenting Rodney kicking in.

"Because," Rodney began stopping once more. "If the wraith ever come in greater numbers- like the entire fleet, we will need the full power of the ZedPM to power the shield, maybe even the cloak- or- should it even come to it, submerge the city all together."

"Ah." John replied with a smile. "Of course."

"Honestly," Rodney began turning back to the ancient device in his hand. "I can't believe that-" At the power readings that he was getting, Rodney stopped and began to look around with curiosity.

"McKay?" John asked with some concern, "Have you-"

"Sheppard," Came the voice of Weir over the comm. "How's it going down there?"

"I have no idea Elizabeth," John admitted. "Rodney, how's it-"

"Sh-shush!" Rodney shushed as he continued looking around, referring to the ancient device as well.

"Elizabeth, we're still looking." John responded. "I'll contact you if we actually find something."

"Very well." Elizabeth replied looking around the control room. "Weir out."

"Do you think that McKay will find what he's looking for?" Ronan asked, stepping up to Weir.

"I hope so." Elizabeth replied. "I hope so."

Meanwhile, back in the north pier, John was totally loosing patience with Rodney.

"Now, McKay…" John began but Rodney held up his hand to shut him up.

"This way-" Rodney exclaimed walking down the corridor to his left, John followed however Rodney had only taken a couple of steps when he stopped and turned around and went down the other corridor. "Sorry, this way."

John just sighed and followed Rodney, hoping that soon this litter excursion to the bowls of Atlantis would be over. Lucky for John, they entered an ancient laboratory that was partially functioning. There was a thin layer of water on the floor, but all the equipment seemed to be un-damaged.

"This is amazing." Rodney exclaimed looking at one of the control panels.

"What is this place?" John asked looking around, dropping his P-90 to his side.

"I have no idea, however…." Rodney admitted going directly over to one of the controls at which point his eyes grew wide with excitement. "Oh, my….this is incredible."

"What?" John asked again, "What is it?"

"Rodney to Elizabeth," Rodney began tapping his communicator, totally ignoring John's questions.

"Yes Rodney?" Elizabeth asked back. "What is it? What have you found?"

"You better come down here and take a look at this." Rodney replied, excitement in his voice.

"Why?" Elizabeth asked.

"Because I think that I've found an ancient weapon."

"Really?" Elizabeth asked intrigued.

"Really?" John asked excitedly.

"Yes." Rodney replied to both of them though he was still speaking to Elizabeth. "So you have to come down here, right now."

"I'm on my way Rodney." Elizabeth replied with a smile, then turning to Colonel Caldwell who was waiting around while his crew repaired some of the damage that was taken in the last Wraith battle, she stated. "Colonel, you have the control room."

"Of course."

Meanwhile, back in the control room, Rodney began pushing some buttons and the panel and display began flashing wildly. John didn't take much notice at first, but it was the frantic muttering of Rodney that got him worried.

"McKay….?" He replied with his military nod as he took a position in the middle of the control room, observing everything.

"The weapon is rapidly building up a charge" Rodney admitted turning to face John.

"And that is a problem because?"

"Because if I can't figure out how to discharge it the explosion could potentially destroy Atlantis," Rodney explained, worry evident on his face.

"Well that's just great McKay." John exploded as Elizabeth entered the room and Rodney went back to studying the panel frantically.

"What's going on?" Elizabeth asked, noticing that the tension in the room and the flashing panel.

"Genius here decided to turn the weapon on, and now it's over loading." John explained waking over to Elizabeth

"Shouldn't we get Zelenka down here?" Elizabeth asked, worried now herself.

"There isn't enough time." Rodney stated. "And it's building up a charge," Rodney explained his voice slightly frantic. "It's not critical yet."

"Same thing." John sniped back.

"No," Rodney began not looking at John. "actually there is a- oh no."

"What is it?" Elizabeth asked beginning to move towards Rodney when suddenly a piece of the panel exploded knocking Rodney off his feet and on to his back, knocking the breath out of him.

"McKay!" John exclaimed, running over to his friend to make sure that he was alright.

"I'm alright." McKay stuttered out, trying to draw a breath. "I'm ok."

"John?" Elizabeth stated in fear as she looked over to the machine which was now going critical.

"Elizabeth," John instantly got up and ran to get Elizabeth out of the weapon's range when the display panel turned red and a white light began to shine from a clear crystal ball beside the control panel. "What the-?" John began looking at the light when suddenly there was a bright flash and the light surrounded the both of them. Rodney had to shield his eyes, and prepared for the end to come, however the light died down, and once Rodney realised that he was alive, he breathed a sigh of relief.

"Ok, not a weapon." Rodney muttered to himself as he struggled to get up, at that point he noticed that both Elizabeth and John were unconscious on the floor. "Oh, great," He muttered again. "I am in so much trouble, Rodney to control room."

"Caldwell here, Rodney is everything alright down there? We observed a massive power spike and thought that the weapon had-"

"It's not a weapon Colonel." Rodney interrupted. "I actually have no idea what it was, but you have to get a med team down here right away, Weir and Sheppard are down."

"Of course they are." Caldwell muttered to himself before he tapped his communication device in his ear (his communicator, like all the others) and contacted Carson in the med lab. "Caldwell to Dr. Beckett."

"Yes Colonel." Beckett responded from the med lab in his Scottish accent. "What can I do for you?"

"You can get yourself and a team to the north pier, Colonel Sheppard and Dr. Weir have been exposed to some ancient device and are in need of medical attention."

"On my way." Carson replied, he motioned to the assistants around him and together they geared up and headed down the north pier.

­

Back in the infirmary, Carson was bustling around the two beds which held Elizabeth and John, both were still un-conscious but they seemed to be stable, however the monitors which showed their brain-waves had Carson very concerned.

"What happened?" Caldwell asked, his arms crossed and his demeanour very imposing.

"I don't know." Rodney responded for what felt like the hundredth time as a nurse bandaged up his arm which had been cut when he fell. "At the time, I thought it was a weapon, but when the panel exploded- I have no idea."

"Well at least you are alright Rodney." Carson replied coming over to them, Ronan and Teyla moving closer to Caldwell.

"What do you mean by that?" Ronan asked. "Are Sheppard and Weir going to be alright?"

"I'm not sure." Carson admitted, explaining what he was monitoring to the group. "All the tests but one indicates that nothing is wrong with them."

"And the test that indicates that something is wrong?" Teyla asked moving forward. "What of that?"

"Well, the one test that shows that something is terribly, terribly wrong is their brain-waves"

"What's wrong with them?" Rodney asked concerned.

"They are exactly the same."

"The same?" Caldwell asked, unsure if he heard Carson right.

"Aye, well, they are almost in perfect sync, it will be only a matter of time before they are the same." Carson confirmed. "And I have no idea how to reverse it."

"Of course you don't" Rodney replied jumping off the medical bed. "But I'll go back down there and-"

"I can't let you do that." Caldwell interrupted.

"You don't have a choice." Rodney snapped. "I won't touch the machine again, all I want to do is see if there are research notes. If there are then I will be able to figure out how to reverse the machine."

"And do what?" Ronan asked.

"And undue what ever has been done." Rodney explained. "Listen, I know I've screwed up, so let me fix it. We need them."

"Go." Caldwell stated as he motioned to the door. "Do what you have to do."

"Thank you." Rodney replied appreciatively as he ran out the room tapping his communicator on his way. "Zelenka I want you to meet me…"

For those who were left in the med-lab, they did not hear the rest of what Rodney said to Zelenka, but all of them assumed that he was asking the scientist from the Czech Republic to join him in the north pier. Meanwhile, Colonel Caldwell made his excuse to Carson and went back up to the control room to monitor anything that was happening there. Teyla and Ronan agreed to stay and watch over them while Carson went back to work studying their scans.

It was hours later when the three remaining Atlantean personal left in the med-lab were alerted to Elizabeth and John becoming conscious again. John groaned in pain first and seconds later Elizabeth murmured something an opened her eyes as well.

"Go get Colonel Caldwell." Carson asked Teyla and Ronan before turning back to his patients. "Colonel Sheppard, Dr. Weir?" Carson began as his two patients began to wake up. "Are you both alright?"

"Carson-" Elizabeth began groggily as she sat up.

"What happened?" John finished for her. Carson looked from John to Elizabeth and then to the display that was monitoring their brainwaves and shook his head. "Carson?"

"That's what I was afraid of." Carson muttered looking from one machine to the other.

"Carson," John began looking at Carson with worry. "-what are you-"

"Afraid of?" Elizabeth finished interrupting John. At this interchange they looked at each other and realised themselves what was going on. "You can-"

"Read my thoughts?" John asked looking at Elizabeth and knowing what she was thinking. "How is that-"

"Possible? I have no idea." Elizabeth answered John's unanswered question. "Carson?"

"Your brain patterns are exactly the same." Carson answered looking at his two patients.

"The same?" John asked in disbelief. "How-"

"Is that even possible?" Elizabeth finished again.

"Okay," John stated looking at Elizabeth. "You have got to st-"

"Stop finishing your sentences." Elizabeth finished. "I know, but it's hard to know what thoughts are mine and what thoughts-"

"Are yours." John finished look at Elizabeth and attempting to shield some of his more personal thoughts from her, but from the strange and slightly shocked look on her face, he had the distinct feeling that he wasn't doing so well. "Carson can you fix this?" John asked ignoring Elizabeth for a moment and found that she too was trying to keep her thoughts her own.

"I'm not sure," Carson admitted. "Rodney has gone back to the north pier in hopes to find some ancient research notes that will tell us how to reverse the machine."

"So I guess it wasn't a weapon." Elizabeth began, looking straight at Carson and ignoring John as much as she could.

"Obviously not a weapon." John muttered.

"Obviously." Carson replied with a slight smile.

"Well I feel fine, can't we-" John began when he felt Elizabeth about to speak up. "No- don't say it, we may be linked but I do not want to spend an undetermined amount of time in the infirmary and Elizabeth, I know that you don't want to be cooped up here again." Elizabeth merely sighed and settled back in her bed. "So how about it Carson, can we get out of here."

"I'm sorry, you certainly can-"

"Rodney to Carson." Rodney's voice interrupted over communications.

"Carson here, what is it Rodney?"

"Are the Colonel and Elizabeth up yet?"

"Aye they are." Carson responded. "Why?"

"Because I need to see how far the link goes" Rodney replied.

"Link?" John asked. "W-"

"What link?" Elizabeth finished.

"What link Rodney?" Carson asked.

"The link that is in them." Rodney replied as he sifted through ancient data. "Listen, your scans wouldn't have picked them up, but there is an added energy source in both Elizabeth and the Colonel that is transmitting their thoughts, that's why their bran-waves are the same."

"So, why do you need them?" Carson asked.

"I need them to walk around Atlantis to see how far the link can go." Rodney replied.

"Great." John replied pulling all the equipment off of him and hopping of the bed. "Elizabeth, you stay here and I'll go pay Rodney a visit."

"John-" Elizabeth warned, worried that something would go wrong.

"Don't say it." John interrupted. "I want to get rid of this link as much as you and if Rodney says that this is the only way then-"

"It is the only way," Elizabeth finished again. "I know, but Rodney was completely mistaken when he thought that what it- what ever it was that did this to us- he thought it was a weapon. Do you really want to go back down there?" Elizabeth asked and as John was about to answer she spoke it out loud for him "Of course you do, it's the only way."

"Right." John nodded. "So-"

"Carson, let him go." Elizabeth interrupted looking from John to Carson. "This is the only way to fix this."

"Very well." Carson agreed half-heartedly. "You can go."

"Thank you." John thanked making his leave of the room when suddenly he stopped and turned to Elizabeth and answered her unspoken request. "I will, you know that."

"You know what?" Carson asked looking at Elizabeth as John left the room. "Elizabeth, what do you know?"

"Nothing Carson." Elizabeth replied. "Nothing."

"Alright," Carson submitted. "If you say so."

"I do." Elizabeth replied with a laugh.

Meanwhile, John was making his way to the north pier when Rodney contacted him.

"Ok Sheppard," Rodney began over the intercom. "What I need you to do is talk to Elizabeth, not with words, but with your mind. Keep doing that till you get down here, I have to see how much range this link has."

"I'll keep that in mind Rodney, Sheppard out."

"Colonel." Teyla remarked running to catch up with him. "Wait."

"Hello Teyla." John remarked as Teyla fell into pace beside him. "What sends you down here?"

"Colonel Caldwell asked me to walk you down there," At seeing the look on John's face Teyla explained why. "Just in case there are any ill effects of this link."

"Speaking of," John began. "I'm going to have to concentrate on this link alight?"

"Of course."

"Thank you, now…" John fell silent and began to talk to Elizabeth with his mind.

'Can you hear me?' John asked in his mind.

'Yes.' Came the resonating voice of Weir.

'Can you hear me now?' He asked a couple metres later

'Yes' The voice of Elizabeth answered again. 'I can still hear you John.'

On and on it went until both Teyla and John reached the north pier and the lab that Rodney and Zelenka were working in.

"Can you still hear her?" Rodney asked as John entered the room.

"Just a sec." John stated before thinking to himself. 'How bout now, can you still here me?'

'Loud and clear John.' Elizabeth responded in her mind as her body just stared into space. 'Loud and clear.'

"Loud and clear McKay." John responded with a smile. "Loud and clear."

"Wow." McKay remarked as he looked from the ancient display to his lap top. "I didn't think that the link would travel this far."

"Really?" Teyla asked intrigued.

"Yes, as a matter of fact-" Rodney began when Zelenka cut him off.

"Actually, it makes a lot of sense," Zelenka began. "You see, I believe that the ancients created this link as a means of communicating silently during times of war. They could do it over great distances, like the Wraith, however unlike the Wraith, not just anybody could tap into it, it would only have worked if you had been exposed to that machine as you and Dr. Weir were."

"Then why wasn't I affected?" Rodney asked, trying to poke a whole in Zelenka's theory.

"Because the panel exploded and sent you flying Rodney," Zelenka explained. "You weren't caught up in that light as Colonel Sheppard and Dr. Weir were."

"Ah." Rodney stated in agreement. "Of course."

"Sounds good to me," John stated. 'Hey Elizabeth listen…'

'I know John.' Elizabeth interrupted, her voice resonating through is mind. 'I heard everything.'

"You can hear what I am saying?" John stated in shock out loud.

'Yes.'

"She can hear what we are saying?" Rodney asked in amazement.

"Apparently." John stated. "What does that mean?"

"It means," Rodney began taking a look over Zelenka's notes. "That the link can go further."

"Much further." Zelenka agreed.

"I don't think that this is a good idea." Caldwell stated sitting in front of Elizabeth, John, Carson, Rodney and Zelenka, with Teyla and Ronan sitting beside him.

"Oh come on." John began, not believing that he wanted to test this out.

"Colonel," Elizabeth interrupted. "This could be a valuable tool against the Wraith, think of it, in dangerous situations, plans could be made simultaneously from great distances, mistakes will be minimized in times of battle. Surely you see this."

"Not to mention the scientific value of seeing how the brain works like this." Zelenka put in.

"I don't want to take the risk." Caldwell responded.

"With all due respect Colonel," Rodney interrupted. "Isn't Elizabeth still in charge?"

"No, actually, the moment that she became incapacitated under an alien influence I was put in charge."

"Colonel." John began, his frustration mounting.

"Sheppard, I am in charge here and I say no, it is a matter of health." Caldwell explained.

"Actually," Carson interrupted. "They are perfect health Colonel, the only thing that is wrong with them is that their brains are working on the same frequency, but so far it hasn't done them any harm. I think that you should let them go, as their doctor I don't foresee a problem."

"Thank you Carson!" John replied giving the doctor a thumbs up.

"Well…."

"Colonel Caldwell," Elizabeth began again, her voice much more authoritative. "How can you not take this opportunity to learn more about the ancients how-"

"Very well." Caldwell interrupted, knowing that he would never get a moment's peace until he submitted. "You have a go."

"Great!" John replied with a smile, nearly jumping up from the table. "Who's with me?"

Minutes later, Sheppard, Rodney, Teyla and Ronan were all in a puddle jumper ready to go while Elizabeth, Zelenka and Caldwell were in the control room, ready to monitor things.

"Control room, this is puddle jumper one, ready to launch" Came the voice of John Sheppard over the comm.

"This is the control room, the roof's being retracted and you have a go for launch." Caldwell responded

"Thank you colonel" John replied over the comm.

'John, be careful.' Elizabeth thought, her stomach in knots and her instinct telling her that this was a bad idea.

'Don't worry Elizabeth,' Came the reassuring voice of John in Elizabeth's head. 'I will be, I always am'

'Of course.' Elizabeth responded with a laugh.

"Dr?" Colonel Caldwell asked turning to Elizabeth at the sound of her laughing.

"Yes Colonel?" Elizabeth asked back, a smile still on her face.

"Is there anything that you want to say to Sheppard?"

"Thank you Colonel, but he already knows all I need to tell him and besides…." Elizabeth started, getting slightly distracted by the conversation starting in the puddle jumper. "-we are going to be in constant contact, in fact… he's thinking that it would be nice if the rood would retract." Elizabeth tapped the communicator, knowing that it would be the only way that she would get Sheppard's attention. "John, if you want Zelenka to do something you have to ask him, you can't just think it."

"Sorry." John responded over the comm.. "Hey, Zelenka could you please retract the roof?"

"Right, sorry." Zelenka apologised pushing some buttons. "Sunroof retracting."

"This is puddle jumper one." John replied over the comm.. "We are on our way."

"Very well, good luck, jumper one." Caldwell responded.

"He says thank you." Elizabeth replied with a smile as she turned to face Caldwell.

"Of course he does." Caldwell muttered under his breath before walking away to check on Zelenka. Elizabeth decided to head back to her office and no sooner had she sat down when Carson entered.

"Can I come in?" Carson asked as he hovered in the doorway.

"Of course Carson," Elizabeth replied with a smile, indicating with her hand that he could sit down in the chair opposite her.

"How do you feel?" Carson asked as he took a seat worried that the experiment would backfire.

"Fine." Elizabeth replied with a smile. "In fact…"

"What?" Carson asked worriedly as Elizabeth's sentence trailed off and her eyes grew wide. "What is it?"

"I can see what he sees." Elizabeth whispered in wonder as she moved her hand and stared intently at it.

"Excuse me?" Carson asked, thinking that he had misheard her. "What did you say? You can see what he sees?"

"Well, not really," Elizabeth explained turning her attention back to Carson. "I see my office and you with my eyes and yet I can see- no sense what he sees. It's like a transparent image in front of my mind."

"What does it feel like?" Carson asked, half intrigued and half concerned.

"I don't know." Elizabeth answered her voice soft and distant. "It's hard to explain, but it is- wow- the beauty of our planet- John's awe…wow….this is incredible" Elizabeth stopped and just sent a thought out to John in the puddle jumper. 'Isn't it?'

'Yes it is.' John agreed as he flew the puddle jumper. He could sense the emotions from what Elizabeth saw. Her comfort in her surrounding, her deep respect for Carson, it was truly amazing.

"Colonel?" Teyla asked noticing that John seemed to be spacing out.

"Sheppard?" Ronan asked tapping John on the shoulder and snapping him out of his slight daze,

"What?" John asked slightly confused for the moment. "What?"

"Are you able to fly this ship?" Ronan asked accusingly.

"What do you mean by that?" John asked turning his attention back to flying.

"What Ronan means," Teyla interjected trying to smooth things over, "Is that we were concerned only because you seemed distracted."

"I am not distracted." John insisted. "I am fully focused on flying this ship- it's just that I can see- no sense what is happening around Elizabeth."

"Amazing," Rodney replied looking up from his laptop. "That's amazing."

"It's more then just amazing." John stated, trying to get his team to understand. "And it's more then just sensing what Elizabeth is seeing, I can actually sense the individual energies in the city and on the mainland."

"Really?" McKay asked even more amazed. "Wow, this could actually be something, uh, McKay to Weir." Rodney stated over the comm..

"Rodney, this is Weir." Elizabeth responded in Rodney's ear. "What do you have for me? John and I are still in contact."

"Yes, I know but listen," Rodney explained really excited. "Sheppard says that he can sense the energies of the individuals on Atlantis and the mainland, I want you to see if you can sense our presence."

"Alright." Elizabeth responded back in her office. "Just give me a second Rodney." Elizabeth allowed her mind to travel to the puddle jumper and did indeed sense the individual energies of those in the puddle jumper. "Yes Rodney, I can sense you all. John is flying, you are taking down data, Teyla is just sitting, wondering how her people doing and Ronan, Ronan is fidgeting."

"Really?" John asked Ronan, knowing what Elizabeth said through the link. "You're fidgeting?"

"I am not fidgeting." Ronan responded coldly.

'John' Elizabeth thought frantically as she expanded her senses and realized that something was wrong. 'JOHN!'

'What?' John asked in his mind and then as the alarms went off in the puddle jumped and he realised what Elizabeth was trying to warn him about, he shot out an initial volley, but it did nothing to the Wraith dart. "Oh, Crap. Hold on you guys." John took the controls aggressively fired a couple of shots at the Wraith dart and then took the puddle jumper in a dive as he tried to elude the wraith dart with Elizabeth's panicked voice in his mind.

"What?" Colonel Caldwell asked running into Elizabeth's office at Carson's call. "What is it?"

"It's a wraith dart." Carson explained as Elizabeth just sat against a wall, frozen in terror. "Apparently it's disabled the puddle jumpers weapons."

"Then I'll put the Dedalaus in the air." Caldwell offered making a move to the doorway.

"No." Elizabeth whispered in fear, her voice soft and shaky. "There isn't enough time, if he's going to make it out of there, he's going to have to do it on his own-" Elizabeth's voice caught in her throat as John's adrenaline washed over her almost smothering her.

'John watch out!' The voice of Elizabeth cried out frantically into John's mind. "It's coming around for another pass.'

'I know.' John thought back as he took the puddle jumper into a roll. 'I'm trying.'

'John!' Elizabeth cried out as the Wraith dart hit the puddle jumped with another shot.

"One more hit and we're dead." Ronan stated warningly.

"I agree." Teyla chipped in. "Colonel Sheppard we have to get out of here."

"And go where?" John asked in frustration.

"Sheppard's right." Rodney agreed. "We can't head back to Atlantis because of we do, the wraith will know that we're alive."

"They already know that Atlantis survived." Ronan pointed out as John managed to avoid another shot by the Wraith.

"If they knew, don't you think that they would have attacked with something more then a dart Ronan?" Rodney asked. "Don't you think that they would have come in greater numbers a lot earlier?"

"Perhaps." Ronan stated sitting back in his seat. "But how do you explain this?"

"I can't." Rodney shouted in fear just as John spun the puddle jumper.

"Would the both of you shut up?" John shouted in frustration. "I'm trying to..."

But John never got to finish his sentence. The Wraith dart finally managed to get a shot past their shields and the consol in front of John exploded and he was thrown against the side of puddle jumper and knocked un conscious.

"Colonel." Teyla shouted as she rushed to John's side. "Colonel."

"He's out cold." Ronan remarked as he helped Teyla get John out of the pilot's chair and into the back compartment of the puddle jumper. "Can you drive this thing McKay?"

"Of course I can." Rodney replied arrogantly as he sat in the pilots seat. "At least I think so."

"Do not hesitate Rodney," Teyla suggested from the back compartment. "Just act."

"Alright." Rodney replied, his voice tight with fear, but the sudden beeping of the consol in front of him got him intrigued. "Wait, what is this?"

"Elizabeth," Carson asked worriedly as Elizabeth stiffened up.

"What is it?" Caldwell asked as Elizabeth's eyes grew wider. "Doctor!"

"I don't know!" Carson shouted back at Caldwell before taking Elizabeth's hand. "Elizabeth are you alright?" But Elizabeth didn't respond, she just stiffened more and then went limp. "Carson to med-lab, get a team up here right away."

"This is exactly what I was afraid of." Caldwell stated harshly at the people in front of him. "This is exactly, what I was afraid of!"

"Would you keep your voice down," Carson chastised the colonel. "I have two patients who need their rest."

"Yes, well I want her out of here right away." Caldwell ordered.

"She isn't a wraith." Rodney defended.

"She was in a dart." Ronan countered.

"She told you her story." Teyla defended, agreeing with Rodney.

"And you believe what she said?" Ronan asked. "And what about him, since when could we trust him?"

"Why should we not believe them?" Carson asked, trying to calm Caldwell, Teyla, Ronan and Rodney down.

"She attacked out people." Caldwell offered as an explanation. "That's why."

"Oh for heaven's sake," Rodney sighed out in frustration. "She only fired on us, because we fired on her first.

"That doesn't matter." Caldwell countered. "What does matter is them. What about them? Sheppard was hurt, as was Weir. This link Rodney, has gone so far beyond a simple mental connection. What happens to one, happens to the other, isn't that right Carson?"

"Aye." Carson agreed with a nod of his head. "If Rodney hadn't gotten here when he did, we would have lost them both."

"Really?" Rodney asked, not realising that he was a hero. "I saved them?"

"Aye- the moment I got the Colonel stabilized, Elizabeth stabilized as well. If he had-"

"Would you all stop talking about me as if I wasn't in the room?" John croaked out from the bed.

"Colonel," Carson stated as he rushed to his patients side.

"Sheppard." Caldwell noted coming to the other side.

"Are you alright?" Rodney asked coming to the end of the bed.

"Yeah, I think so…" John replied placing a hand on his head, which was still throbbing severely. "What happened?"

"John," Came a weak voice from the bed next to John.

"Elizabeth?" John asked struggling to get up and see Elizabeth, Carson moved aside and allowed the two of them to look at each other.

"What-" Elizabeth began.

"Wraith." John explained, knowing that much.

"And your team-" Elizabeth asked, but left the question hanging, known that John knew what she was thinking.

"Fine." John assured. "We're all fine, I think."

"Yes Colonel Sheppard." Carson interrupted. "You and your team are all fine."

"What happened to the Wraith?" Elizabeth asked the rest of the team knowing that with this question, John would not have known the answer.

"Actually, surprisingly, not a Wraith," Rodney replied.

"What?" John asked in surprise.

"Really…" Elizabeth stated in wonder.

"Then what was it that attacked us Rodney?" John asked the scientist, hoping to catch him.

"Uh, me." Came a small voice from another hospital bed.

"And who is-me?" John asked, his voice changing in surprise as a small, petite and beautiful human stood in front of him. In his mind, he could feel Elizabeth putting up a wall, but for the moment, he didn't care. "Who is she?" John asked turning to Rodney. "Who are you?" John asked again turning to the girl.

"I am Quitha." The girl replied, her soft golden hair around her shoulders and her ice-blue eyes shining with light. "I am truly sorry for shooting at you Colonel Sheppard, but you must understand, you attacked me first and I thought that you were the Wraith in a new type of cruiser."

"No," John replied with a laugh. "No, we are defiantly not the Wraith."

"I know that now." Quitha replied, her voice soft and kind.

"How did you get onto the dart Quitha?" Elizabeth asked, her instincts telling her not to trust this girl, but her mind telling her that it was illogical to doubt her at this time.

"My entire village was culled," Quitha began, her eyes misting up with tears. "-as was I. When I awoke, I awoke on a hive ship. I watched as all I knew were fed upon by those monsters until I was the only one left. When my time came, the Wraith could not feed upon me.' Quitha closed her eyes and pictured the image of the wraith placing his hand to his chest and roaring in anger. "Once he realised that he could not feed upon me, he left." Quitha continued pulling herself out of the horrible memory. "After that, I fled and found someone who could help me."

"And who might that be?" John asked, intrigued.

"Me." Came the voice that John recognised very well.

"Ford?" John asked in surprise as Lieutenant Aiden Ford came into his line of vision. "Ford!"

"Lieutenant!" Elizabeth remarked in surprise.

"Ma'am, Sir." Aiden acknowledged respectfully. "I'm sure that you're wondering how I got off that Wraith hive when it exploded."

"The thought did cross my mind." John replied indicating that he wanted Aiden to continue.

"Well," Aiden began remembering what had happened to me. "I managed to make my way to the dart bay just as the ship was beginning to explode. I got in one and surprisingly it's shields protected me. However, it's auto-pilot engaged, and I found myself entering a new hive ship. They put me in one of those damn cells and tried to get information out of me. Of course, I got too weak to answer, and they finally decided to feed on me. But they couldn't, there was still too much enzyme in my body. They drew it out of me that I had been attacked by a wraith and his enzyme had been sustaining me, that's when they gave me the deal" _"We will give you the enzyme you require, as long as you provide us answers for our questions."_ The wraith's voice haunted Aiden's head, but he continued with his story. "Of course I didn't agree. I would have rather died then given up the secrets that we had worked so hard to keep, but eventually I got to a state of delirium and I agreed. I told them that I was the lone survivor of the Atlantis attack and that I was the only one who had managed to get through the gate as it exploded, with the wraith attached to me. The wraith died, and I got the enzyme."

"And they believed you?" Elizabeth asked in awe.

"Yes ma'am." Aiden replied rather pleased with himself. "I told them that once I got the Wraith off me, I tried to dial Atlantis but that the last chevron wouldn't engage. That convinced them that you had been destroyed. I then told them how I had been a rouge fighter, that I had been killing their kind for their enzyme. This they didn't like, and while they kept giving me what I required to survive, they began to cut down my dosage."

"That's when I found you." Quitha pitched in.

"Yes, Quitha came by and together we made it to the dart bay. I was too weak at this time and told her what she needed to do to fly the ship." Aiden explained.

"Really?" John asked, surprised.

"Yeah," Aiden confirmed. "She got into the ship, beamed me up and we headed to Atlantis."

"And when you attacked me," Quitha continued. "I panicked, I forgot that Aiden had told me that I should expect to be attacked, it was only after you started to run away that I realised who you were and I remembered what Aiden told me and I hailed your jumper and explained who I was."

"That's where I come in." Rodney interjected. "After you were rendered unconscious, I successfully got us back to Atlantis with Quitha and Ford in tow."

"I am truly sorry." Quitha apologised.

"That's quite," Elizabeth began.

"Alright." John finished his voice calm and quiet. "Lieutenant?"

"Yes sir?" Aiden asked jumping to attention.

"Good job back there." John praised.

"Where sir?" Aiden asked, not knowing what John meant.

"On the hive ship, you watched out backs." John explained, with a smile on his face. "Good job, thank you."

"Thank you sir." Aiden thanked. "You're welcome sir."

"Now," John stated, changing the subject "Why-"

"Am I here?" Elizabeth finished. "I remember feeling immense pain, and then- nothing."

"I believe that Carson can explain that." Caldwell interjected.

"Aye." Carson agreed. "The energy that was between you has been stretched to the limit. When Colonel Sheppard was rendered unconscious, it snapped and you Elizabeth felt the result."

"So that's why I fainted." Elizabeth stated, understanding.

"It was my fault?" John asked, slightly taken aback that he had done something to cause Elizabeth pain.

"Indirectly." Carson explained. "The connection isn't gone, it's just immensely weak now- that means that, well, Rodney?"

"Which means," Rodney explained, his voice grave. "that the two of you will need to stay in extreme close proximity for the next little while."

"How close?" Elizabeth asked, curious to know.

"I'd say, that if you get anymore farther apart then you are now, you'll both die." Rodney explained.

"Die?" Elizabeth asked in horror.

"Rodney," John warned. "You have to fix this- not that I don't mind spending time with you Elizabeth-"John stated, putting Elizabeth's objections about being not wanted. "-it's just that we have out jobs to do."

"I know." Rodney stated.

"So fix it." John ordered. "Put us back through the machine, reverse what happened."

"I can't." Rodney denied.

"Why not?" Elizabeth asked, her like John not understanding why Rodney just couldn't put them through the machine again and reverse the connection. 'Not that I actually want the connection gone.'

'Really?' John asked, looking at Elizabeth with confusion in his eyes.

"Are you two listening to me?" Rodney asked, noticing that Elizabeth and John were no longer paying any attention to him.

"Sorry." Elizabeth apologized, closing her mind off to John.

"What were you saying?" John asked.

"I was saying, that this machine was used for long-term reconnaissance between the front line and Atlantis." Rodney explained. "I can't reverse it because the machine wasn't built for that, in fact the Ancients stopped using it."

"Why?" Elizabeth asked, trying to keep her mind off John.

"Because the ancients found that the device was addictive." Carson explained for Rodney.

"Addictive?" John asked in horror.

"Don't worry," Rodney eased. "The ancients found that to keep the connection, they had to be continually exposed to the machine, that's how they found it addictive, and they began dependant."

"Will we be like that?" Elizabeth asked. "Will we be dependant?"

"No." Rodney confirmed. "From everything that I've read says that one dose will wear off in about twelve more hours at the most. The point is, we should permanently lock that room to prevent anyone getting addicted"

"Agreed." Elizabeth replied nodding.

"Agreed." John replied as well.

"Colonel Caldwell," Elizabeth stated changing the subject. "You are in charge until we are back to normal."

"Of course." Caldwell agreed. "Come on everyone, we have to get back to duty, the wraith might be headed our way"

"What?" Elizabeth asked in alarm.

"The Wraith are headed our way?" John asked, in horror. "How?"

"They aren't," Aiden insisted. "Jeez how many times do I have to say this, they think that Atlantis was destroyed."

"Yeah?" Ronan asked, "And how do you know that?"

"Well, I was their captive for months," Aiden stated. "I think I would know, you believe me sir, don't you?"

"Of course I do Ford," John agreed. "But just suppose for a moment that a hive ship followed you and Quitha here,"

"They didn't." Quitha insisted.

"Yeah," Aiden agreed. "I think we would have known if the Wraith had followed us."

"All I'm saying is that if –"

"Actually, you were saying suppose." Rodney interjected.

"Rodney-" John warned.

"Sorry." Rodney apologized.

"What the Colonel is saying Lieutenant," Elizabeth interjected trying to keep the situation calm. "-is that we should let our people do the jobs that have been assigned to them in order to keep us all safe."

"Our people ma'am?" Aiden asked, slightly taken aback.

"Well," Elizabeth began with a smile. "You are Lieutenant Aiden Ford, are you not?"

"Uh, yes ma'am." Aiden agreed.

"Well then, the personal of Atlantis are your people as well, after all-" Elizabeth continued with a smile. "You did come here from Earth with the rest of us three years ago, therefore you belong here with us."

"Yes ma'am." Aiden replied with a smile. "Thank you ma'am."

"Oh!" Carson interjected moving towards Elizabeth and John. "You'll both be pleased to know that the Lieutenant is almost completely weaned off the drug."

"Really?" Elizabeth asked intrigued.

"How?" John asked.

"Well, the Wraith were cutting down my dosages of the enzyme." Aiden explained. "They wanted to kill me and be fulfilled knowing that all Atlantis personal was destroyed, but they couldn't feed on me how I was. They were patient, and they gave me smaller and smaller dosage until Quitha saved me." Aiden looked over at the young beautiful women and smiled and was pleased when she smiled back.

"What Enzyme I have left will be more than enough to wean him off the rest." Carson responded with a smile.

"Excellent." Elizabeth commented. "Colonel Caldwell-?"

"Yes Doctor?" Caldwell asked coming up beside Elizabeth.

"With our sensors out of commission due to that virus, how are you going to determine if the wraith are coming or not?"

"I think it would be best if we took the Orion and the Dedalaus to check it out." Caldwell suggested.

"That'll leave just a few personal on base." John pointed out.

"That's right," Rodney pointed out, worried now. "What if something happens while the two ships are out there."

"Rodney, what are the odds that the Wraith or another enemy will attack when they're gone?" Elizabeth asked, trying to calm her own fears as well as Rodney's.

"Uh, quite slim actually." Rodney stated, knowing that he would be defeated.

"Alright," Caldwell assured getting everyone's attention. "Let's go people, we've got work to do."

"Uh- Zelenka and I will remain behind," Rodney began. "There are a few things that will need doing from this end."

"Very well." Caldwell agreed before motioning to everyone to leave.

"Come on Quitha," Aiden replied taking Quitha by the hand. "I'll show you the rest of the city."

"I'd like that." Quitha responded with a smile and followed Aiden out of the infirmary.

"There's something about Quitha that I just don't like." Elizabeth muttered to John once Ford and Quitha were out of the room.

"Oh, come one Elizabeth," John stated with an exasperated sigh. "She doesn't seem that bad."

"Seem?" Elizabeth asked with a hint of hurt in her voice. "Or look."

"Elizabeth," John replied, his voice a mixture of apologetic shock. However Elizabeth didn't respond she just rolled over and attempted to fall asleep, all the while praying that John couldn't hear her thoughts- which for the moment, he couldn't.

"And this is the control room." Ford stated as he lead Quitha into the control room.

"I know." Quitha stated with an evil look in her eye as she pulled out a mini gun and shot all who were around her. Rodney was first and he managed to hit the lock out button before he was hit. Quitha hit a button on bracelet that she had around her wrist and the clear jewel began glowing purple and green. She noticed Rodney and with a growl, Quitha shoved Rodney off the consol and attempted to get it up and running. After several moments, she growled again and left to get the only people still awake that could help her complete her goals.

They had been silent for what seemed like hours, however John knew that it had only been thirty minutes or so. Carson had disappeared on what was called a medical emergency and he ordered Elizabeth and John to stay put while he left. Elizabeth and John were now alone, and he was still feeling guilty over what he said, and he got up the courage to bring up the subject with Elizabeth.

"Elizabeth?" John asked sitting at the edge of his bed, looking at Elizabeth's back.

"Yes?" Elizabeth responded, not turning to face John.

"Listen, I just wanted to-" John never got to finish his sentence because it was cut off by the sound of an explosion.

"What was that?" Elizabeth asked with a start as she sat up in her bed and looked frantically at John.

"I have no idea." John admitted reaching for his radio. "But I'm going to find out….Sheppard to Caldwell, come in Caldwell." John waited for a moment but only got static. "Sheppard to Rodney." John waited for another few moments but again got nothing but static. "Teyla? Ronan? Zelenka? Ford?" Each name he called he waited, but received nothing but static. "This is Colonel Sheppard to any Atlantis personal, please respond."

"Sir," A lieutenant whom Sheppard knew was new responded; his voice frantic and gunfire going off in the background. "It's the-" The Lieutenant was cut off by more gunfire and the line went static.

"Oh, this is not good." John muttered to himself getting out of his bed and as he turned towards Elizabeth. "I'm going to see what is going on."

"Not with out me your not." Elizabeth responded as she too got out of the bed.

"Elizabeth, it's too dangerous, I'm not about to-"

"John." Elizabeth soothed. 'The link.'

'Oh' John thought, slightly embarrassed. "Well we'll hit the armoury first. But stay close." John ordered as they headed towards the door. "I don't want you too- Quitha! What a pleasant surprise, we were just going to see what the explosion was- um"

"Stay where you are." Quitha interrupted as she moved forward with a hand gun, causing John to bump into Elizabeth. "And be silent."

"John," Elizabeth stated warningly, hearing the change in Quitha's voice. "She's a-"

"Wraith." John finished, feeling completely stupid because Elizabeth had sensed something wrong and he hadn't. "I figured that out."

"You are observant." Quitha responded, her voice changing even more into a Wraith, and her features changing too. "Now, you-" She began, pointing to Weir. "-will come with me. And you," Quitha continued pointing to John. "Will go with them."

"And who might-" John began but stopped when he saw two large Wraith soldiers come up behind Quitha with large stunners in their hands. "Never mind." John muttered looking back at Elizabeth.

"Be silent." Quitha ordered. "And come with me." She moved to grab Elizabeth but Elizabeth jerked away just as John intercepted them.

"She can't." John stated moving Elizabeth behind him.

"And why is that?" Quitha asked, looking most displeased.

"We are linked together." Elizabeth explained standing beside John. "Our minds our linked together and if we are separated we will die."

"How is this possible?" Quitha asked looking from John to Elizabeth.

"It wasn't intentional." John defended, not liking the look that Quitha was giving them.

"No, it wasn't." Elizabeth agreed. "We were exposed to a device that was created by the Atlanteans. That is what caused the link."

"Very well." Quitha stated, not looking happy. "You both shall come with me." Quitha exited the door frame and allowed her two foot soldiers to pull Elizabeth and John into the hallway. Quitha then took the lead and they began walking.

"If I may ask," Elizabeth began shortly after leaving the infirmary. "Where are we going?"

"To your control room." Quitha answered not looking back at her two prisoners.

"And why are we going there?" John asked catching up to Elizabeth and walking beside her.

"Because we are locked out of the system, and I need the two of you to get us into the Atlantean mainframe." Quitha answered.

"And if we don't do what you ask?" Elizabeth asked, hoping that the consequences wouldn't be too dire.

"Then I will kill all of the personal left on this base," Quitha explained. "After which I will feed upon one of you, and watch as the other dies."

John and Elizabeth just looked at each other worriedly and knew that they would need a miracle to get out of the situation that they found themselves in.

A few minutes later, John and Elizabeth were heading towards the control room and they were silently trying to figure out a plan to regain Atlantis from the Wraith.

'John," Elizabeth thought.

'Elizabeth,' John responded, keeping his head straight like Elizabeth was doing.

'The link is getting stronger.'

'Yeah,' John agreed. 'I noticed that- why do think that is?'

'I have no idea,' Elizabeth admitted.

'This could come in handy. We could-' John thought excitedly

'We have no idea if we will be able to test this- us dying will not be a good thing for us or Atlantis. We defiantly do not want the wraith to get to Earth.' Elizabeth thought back quickly.

'Right,' John agreed, mentally kicking himself for being so stupid. 'But he have to something.'

'I know.' Elizabeth agreed.

'Maybe if we-' John began when suddenly there were shots fired at the wraith. 'What the-?' More shots were fired and John pulled Elizabeth to the ground to protect her.

"Are you two alright?" Came a familiar voice.

"Ford?" John asked looking up.

"Are you alright Colonel?" Aiden asked again watching as John and Elizabeth shared a look.

"We're fine." John replied looking from Elizabeth to Aiden and then to Elizabeth again, who in turned looked at her.

"Good," Aiden stated relieved. "-let's go."

Minutes later John Elizabeth and Aiden were still making their way through the city.

"What happened?" Elizabeth asked as they were walking away.

"Why didn't you kill the wraith?" John asked, thinking that his question was more pressing.

"It wouldn't have made a difference Sir," Aiden explained. "They culled an entire planet before coming here, nothing short of blowing them up will stop them now."

"I see." John stated, not liking where this was going.

"Lieutenant, what happened?" Elizabeth asked, wanting an answer to her question.

"It was Quitha ma'am." Aiden explained. "She tricked me, I thought that she was a human, but she's a-"

"Wraith." John interrupted. "Yeah, we kinda figured that out."

"Yeah," Aiden agreed. "I did not see her coming, she knocked me out."

"The question is," Elizabeth began. "- how are we going to stop her?"

"Oh, we are going to have to stop a lot more then just her ma'am." Aiden replied solemnly and let John and Elizabeth to a window that over looked the city where they saw the most horrible sight. There above Atlantis were about twelve hive ships that they could see and both John and Elizabeth knew that there were probably many more around the city.

"Dear God." Elizabeth whispered walking towards the window.

"This could be a problem." John whispered joining Elizabeth at the window.

"A big problem." Elizabeth confirmed.

"Come on," Aiden interrupted. "We have to keep moving."

"Right." John agreed and slowly he led Elizabeth away from the window and they followed Aiden through the city.

While John, Elizabeth and Aiden walked around the city trying to get weapons, the rest of the senior staff awoke in the cell that they had held their Wraith prisoners in.

"Rodney, Rodney?" Teyla called shaking Rodney and trying to get him awake.

"McKay." Ronan shouted which caused Rodney to jump up.

"Huh-? What?" Rodney asked jerking awake.

"Are you alright?" Teyla asked concerned.

"No-" Rodney admitted putting a hand to his head. "Ugh- what happened?"

"The Wraith." Ronan explained helping Rodney to sit up.

"Really?" Rodney replied in shock, having a moment of temporary amnesia.

"Yes," Carson agreed. "It was defiantly the wraith, the marks on Lt. Tannis were un-mistakable."

"But who-?" Rodney asked in shock and fear. "How-?"

"I believe it was Quitha." Teyla replied solemnly.

"Or Ford," Ronan suggested.

"No," Zelenka interrupted. "It was defiantly Quitha."

"And how do you know that?" Ronan asked.

"No," Rodney interrupted. " Zelenka's right- Ford had nothing to do with this."

"And you know this McKay because….?" Ronan asked.

"Because I was in the control room when she turned on us, I was able to lock out the mainframe before I was hit- and Quitha attacked him first, then all of us." Rodney explained clearly quite proud of himself that his memory had returned.

"Then what happened to Lieutenant Ford?" Carson asked.

"I have no idea." Rodney admitted. "But I do know that Ford look absolutely shocked when the Wraith stunned him, he can't be working for her."

"Hey Ford," John began as they left the armoury. "Can I ask you a question?"

"Go ahead sir."

"I assume that everyone on Atlantis has been locked up?" John asked, trying to piece together what was happening and how it had happened.

"I think so sir," Aiden explained. "They are either in the cell or locked up in their rooms, before I found you I went through the personal quarters and heard some banging but neither I nor those inside could get the doors working….the senior staff seem to be in the cell because non of them were in their rooms."

"Alright," John began, trying to put things together. "So how did you escape?"

"Well sir," Aiden began, "-when Quitha stunned me, it didn't completely work. I was totally conscious when I fell, but I was almost totally paralyzed, but it wore off quickly and while Quitha started dragging people away, I managed to drag myself under a control consol where I waited while she was letting Wraith come into the city. When she finally left the gate room unguarded, I was able to escape."

"But that doesn't explain how the hive ships were able to circle Atlantis in such a short time." Elizabeth began. "I mean our sensors were damaged, but even in their damaged state they would have picked up that many ships."

"Actually it does," Aiden began again. "See- last time they attacked, they sent meteors to disable our mines, which also affected our sensors, now McKay said that every 100 years or so, Atlantis gets hit with a severe meteor show, the Wraith would know that because of the first siege with the Atlanteans, so they just waited till this meteor shower came and waited till it had passed through our system then, knowing that our sensors would down not only from the shower, but the virus which I hear was from a wraith module- they must have banked on the fact that we would have problems getting it up and running again so they've been waiting."

"But that was weeks ago." Elizabeth pointed out.

"I know, that means that the Wraith have been planning this for a long time ma'am" Aiden finished.

"We have to finish them off once and for all." John stated as they kept on walking.

"Yes," Elizabeth agreed. "But how? Our drug doesn't work- we can't get it to spread fast enough though their systems- and it's not like we can do anything now especially with the Orion and Dedalaus out there."

"What about the Orion and Dedalaus," John thought, speaking aloud. "What if we could get a message to them?"

"Sir, I doubt that even they could take out that armada." Aiden pointed out.

"Really?" Elizabeth asked shocked. "I thought that the Orion had a whole arsenal of drones."

"True," John agreed. "But most of them are in the lower sections of the city along with the ones that we brought from the planet with the tower for the chair…."

"The chair!" Elizabeth exclaimed excitedly.

"What chair?" Aiden asked confused.

"We have a chair like the one in the Antarctic base." Elizabeth began.

"And now, with a ZPM," John continued.

"We'll be able to power it up and save the city." Elizabeth finished.

"Now we're talking." Aiden said with a laugh.

"Come on," John interjected. "We need to get down to the chair room as soon as-" John was cut off by the sounds of the city alarm system going off. "Now, what?"

Meanwhile, the control room was swarming with wraiths who were trying to unlock the cities main-frame when suddenly they found themselves trapped.

"Oh no…" Elizabeth whispered, listening as the bulk heads around them started to close.

"Run!" John ordered and led the way to the chair room with Ford right behind him and Elizabeth bringing up the rear when suddenly the bulkhead behind them separated them.

'John' Elizabeth cried in horror, watching through the glass of the door as Aiden and John got stuck in a small room with stairs leading down.

"Elizabeth.' John thought in horror as he ran towards the bulkhead.

'John, now what are we going to do?' Elizabeth thought worriedly.

Meanwhile, down in the cell room, those trapped in there were beginning to react to the alarms that were sounding.

"Oh, now what?" Rodney asked standing up.

"I-" Zelenka began, only to be cut off by Rodney.

"Shhh!" Rodney ordered and everyone fell silent and heard the horrible sound of bulkhead doors closing. "Oh no…"

"What is it?" Ronan asked confused.

"The city is locking down." Rodney admitted putting his hands to his head trying to think.

"What?" Teyla asked in horror.

"How is it doing that?" Carson asked.

"Listen," Rodney interrupted. "Zelenka and I planned for this- in the unlikely eventuality that the Wraith would get this city intact, we created a virus to act like a contagion, so if the Wraith started messing around with Atlantean controls-"

"Atlantis would think that a contagion has been released into the city." Zelenka finished.

"Exactly." Rodney stated.

"And what will this do exactly?" Ronan asked.

"This will ensure that all the wraith in the city will be trapped where they are and that no wraith will be able to beam in." Zelenka explained.

"And how is this a problem?" Ronan asked again.

"This is a problem because Elizabeth and Sheppard, who are our only hope of getting out of here will be trapped as well." Rodney explained.

"If they haven't been culled yet." Ronan stated as he sat down on the bench.

"Let's think positively shall we?" Carson interjected.

"Oh they're alive." Rodney stated grimly.

"How can you be sure?" Teyla asked.

"Well I can't-" Rodney admitted. "But the Wraith seem to want us to actually see the destruction of Earth, which is probably why all of us here are still alive- and besides with the computers locked out Quitha will need them to override the system."

"Right." Carson agreed. "But what if they were separated?"

"Oh this is a problem." Rodney muttered. "Oh, this is so not good!"

"So what do we do?" Ronan asked standing up again.

"Nothing." Rodney stated fear and anger lacing his voice. "Absolutely nothing! We are trapped in here and Elizabeth and Sheppard are out there! If they have been separated by more than a single bulkhead then it is only a matter of time until they die and then our only hope of sending a message to Caldwell, taking back the city and saving earth will be gone. Completely gone."

After Rodney's outburst everyone in the cell was deadly quiet.

"If that is so," Teyla stated after a few moments of them all looking at each other. "Let us pray to the ancestors to ensure that they are alright."

"Elizabeth!" John called pounding on the door.

"John!" Elizabeth replied, pounding on the door as well.

"Sir," Aiden interrupted. "We've got to-"

"Ford just go." John ordered. "Try to contact our ships, or even better go find Rodney so he can fix this damn door which I know is his problem."

"Sir I-"

"Go Ford!" John ordered again. "That's an order."

"Yes sir- but" Aiden began again.

"Aiden!" John exploded causing Elizabeth to jump back slightly at the emotion in his voice and his mind. "I can't leave her."

"Understood sir." Ford replied and after a salute, he scurried down the stairs to find Rodney.

"Elizabeth?" John asked turning his attention back to the door. "Are you alright?"

"Yes," Elizabeth confirmed. "I think so…..but how am I going to get out of here?"

"I don't know," John admitted placing his hand on the transparent coloured glass and watched as Elizabeth did the same. "Ford's either going to contact our ships or he's going to go bust Rodney's butt out of where ever he is and get him here to help us."

"John, we have to get me out of here." Elizabeth stated. "We have to go stop the wraith, if they manage to override the lockdown…"

"I know," John interrupted thinking the same thing as Elizabeth. "I just don't know how."

"I know that you have to arrange the crystals in the panel beside the door in a certain order." Elizabeth offered.

"Do you know what order?"

"No." Elizabeth admitted. 'But I should, I've been in Atlantis for three years now.'

'Don't blame yourself.' "Do you know if we have to do this on my side or yours?" John asked again.

"No," Elizabeth admitted again.

"Well then-" John began stepping back to look at the panel beside him. "Let's see if I can…." But Elizabeth never heard what John had said because his words were cut of by the sound of Wraith stunners and P-90 bullets being fired.

"John?" Elizabeth asked in fear when suddenly she jumped because there were shots being fired at her. Elizabeth quickly ducked and managed to kill the two Wraith that were struggling to get though the partially open bulk head. Once they were sufficiently dead to Elizabeth she shoved them back into the other sealed section, closed the bulkhead and shot the panel with the crystals to stop them from sneaking up on her again. Once that was done she was back at the other door that separated her from John in a heart beat. "John? John?" Elizabeth asked out loud fear gripping her heart each moment that he didn't reply to her, she pressed her face to the glass in an attempt to see him, but she couldn't see much of anything- which greatly worried her.

'JOHN!' She cried out frantically with her mind but met nothing. 'I'm not dead, He can't be dead, unless-' Elizabeth stopped that strain of hopeful thought. '-unless the link has worn off.' "Oh my god." She whispered to herself in horror. 'How long has it been? Oh god, JOHN!' Elizabeth cried out in her mind and out loud! "JOHN!" But there was no answer and Elizabeth knew that she was wasting precious minutes but her brain couldn't get an idea together

Meanwhile Aiden was running though the hallways, opening bulkhead doors "Thanks to McKay" he muttered, freeing some Athosians and as the new party was making their way to the main cell they became cornered with Wraith

Meanwhile aboard the Dedalaus and Orion, both of which were badly damaged and dead in the water, Colonel Caldwell was trying to get a bad situation under control

"Get those systems up and running, we have to save Atlantis." Caldwell ordered and nodded grimly as various technicians and scientists replied "Yes Sir". Caldwell then turned back to the task of contacting Atlantis. "Caldwell to Atlantis, come in… Atlantis please respond…."

Meanwhile, Elizabeth was still frantically calling John's name both through the door and over her communicator (neither of which seemed to be working).

"John! John!"

**End of Part 1**

A/N- Alight, so not the update that I am sure you all wanted, but as I was writing part two, I realised that it would be too long so I went back from my original split point. This is where it was meant to end, here- with a cliff hanger- so enjoy. Hopefully Part II will be up in a week or so I hope you like the new part. Part II will be out soon. I swear


	2. Battle for Atlantis

Disclaimer: None of these characters are mine, I wish they were, but they aren't. This story is has Sparky undertones…..ok Sparky overtones- but if they could do it for Long Goodbye then I can do it for this!

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Stargate Atlantis.

Sometime in season 3, perhaps the end of the season, maybe a cliff hanger.

A/N: 'thoughts' "dialogue" scene changes

**Battle for Atlantis**

**Part 2**

"John, John!" Elizabeth cried pounding on the door, and then in a flash of clarity she realised that she had to open in by using the small panel to the left of the door. With shaking hands she pried open the cover and began moving the crystals around, praying that each one she moved would open the door. 'Come one Elizabeth, you can do this.' Elizabeth chastised herself as each time it didn't work she got more and more panicked.

Finally Elizabeth managed to get the door open and she immediately ran into the small room with the stairs and saw John leaning up against the wall with the panel with the door with blood running down his head and out of his right shoulder.

"John," Elizabeth whispered in horror. "Oh my god."

Meanwhile, back in the cell Ronan, Rodney, Zelenka and Teyla heard shooting from outside.

"Someone's coming." Ronan stated standing up, prepared to fight.

"Hopefully it will be someone who can help us." Teyla stated with grim determination on her voice as well and unknowingly all held their breaths as the cell room door swung open and the person shooting was revealed.

"Ford!" Rodney exclaimed with shock.

"McKay," Aiden greeted. "Looks like I'm saving your butt."

"Look like." Rodney replied.

"Come on," Aiden ordered once the cell was open. "Colonel Sheppard and Dr. Weir are trapped."

"Together?" Carson asked worriedly.

"No," Aiden answered and watched as all the faces fell.

"How many bulkheads were between them?" Rodney asked, not wanting to know the answer.

"Only one." Aiden replied.

"Only one?" Rodney asked in shock.

"Then they may still be alive." Zelenka stated, his hope starting to grow.

"No, they will be alive." Rodney confirmed with joy.

"Where are they trapped?" Carson asked, concerned for his patients.

"This way," Aiden indicated. "But hurry, they may be hurt."

"You don't know?" Carson asked again.

"No," Aiden admitted. "Sheppard ordered me to come here and rescue you guys and on my way here I thought that I heard gun fire."

"You thought?" Ronan asked following Sheppard.

"Never mind this now." Teyla interjected, "Let us get to where they last were as quickly as possible."

"Right" Aiden agreed.

"Let's go." Ronan stated and together; Ronan, Rodney, Teyla, Zelenka, Carson and Aiden all retraced Aiden's path.

Meanwhile, Elizabeth was still trying to get John to regain consciousness.

"Come on John," She begged bandaging his shoulder and pressing a cloth to his head to try and stop the bleeding. "John? John please…."

'Elizabeth?'

"John?" Elizabeth asked placing a hand on John's face which moved as he regained consciousness.

"I'm here." He muttered as he struggled to sit up, which Elizabeth helped him with after which she hugged him as tightly as she dared.

"Oh thank god." She muttered into his ear. "I thought I'd lost you….again."

"Again…?"

flashback

They had just gotten to Atlantis, John was going to rescue his people and above the gate the ceiling opened and the puddle jumper slowly descended until it was in line with the gate after which it moved forward through the event horizon and Elizabeth remembered standing with Rodney and whispering to them all, but John in particular "Be safe."

Then it was later and she was standing in the gateroom staring at the Stargate, her heart was fluttering in fear and she had a knot in her stomach and she wasn't even paying attention to Rodney and when he trailed off she spoke. "I should have never let them go."

"For what it's worth," Rodney replied sympathetically. "-you made the right decision. Give them time."

Then, later the gate started dialling in, "Off world activation" Grodin stated. "Raise the shield." Elizabeth ordered, the fear getting worse. Moments passes and Elizabeth found herself speaking again. "Do we have an identification code?"

"Nothing yet." Rodney replied as he checked his laptop.

And then moments later Rodney spoke the words that she wanted to hear. "I'm reading Lieutenant Ford's I.D.C."

"Let them in." Elizabeth ordered, the knot in her stomach unwinding a little as Grodin hit the control to lower the shield when suddenly they were under fire and though they were all diving under consoles Elizabeth found herself shouting over the noise "Give them a few more seconds" And a few seconds later, the puddle jumper came racing though the gate and stops and Elizabeth shouted, "Reactivate the shield." She looked down into the puddle jumper and smiled with relief as she saw John sitting there in the drivers seat.

It was weeks later and she was in the gateroom, the Stargate was open and the Atlantean alarms were sounding. "What's going on?" she asked, a horrible feeling growing in the pit of her stomach, one of her team was hurt and as the technician finished she asked for the technician to put on John and then she got the worse news that she could. "He's the one who's injured," once those words left the technicians mouth, her heart dropped to her stomach.

She was then patched through to the jumper, she asked what was the nature of the major's injury and she listened with a horrible growing feeling as Ford explained to her what it was. She found herself asking what it was doing to John and when Ford answered that they didn't know and that they couldn't get it off, even after trying everything she started to panic but she knew that once they were through the gate Carson would take care of him.

But then, they weren't coming through, the gate was active and everything indicated that they should have been through and she was left to watch and wait and when they finally got in touch with the jumper, she learned that they were stuck in the Stargate. Then while she was learning what was happening, she learned of the time limit.

"And we have less than thirty eight minutes" Rodney interrupted causing Elizabeth's heart to stop.

"Hold on," She stopped trying to understand. "Why thirty-eight minutes?"

Then she was told why and she scrambled her scientists and put them on the task. And she found herself trying to keep everyone up. "Let's not admit defeat just yet, Doctor. There are six people on that ship."

'Six people,' Elizabeth thought fearfully. 'Including John."

Elizabeth found herself getting back to work and she irritably had to break up a fight between Kavanagh and Simpson. She snapped at Kavanagh and while she was listening to his concerns her back became raised and she was near livid.

"I thought it was important to point out the risk." Kavanagh pointed out.

"Fine." Elizabeth snapped. "You did, now please- worry a little bit more about _their_ lives and less about your own ass…" She checked her watch and updated the scientists on the time. "Twenty-three minutes."

Elizabeth left them and then was ambushed by Halling and he to got her irritable and she had to get away from his concerns. "I'm sorry. I can't have this conversation right now?"

"Why not?"

"Because we are wasting time!" Elizabeth stated turning back to Halling.

"This is time that Teyla could use to prepare."

"Alright," Elizabeth interrupted, her patience wearing thin. "You perceive death a certain way. I accept that. In fact, I respect that. But we do _not_ prepare for dead. _We _do everything we can to stave it off. That is who we are.

It was later, when she had her run in with Kavanagh and she found herself giving the scientist an ultimatum. "No, your missing mine. If you waste one more minute which could be used to help the people trapped on that ship because of your ego, I promise you I will dial the coordinates of a very lonely plaent where you can be as self important as you want to be….You think I'm kidding?"

"You wouldn't do that."

"Kavanagh, get back in there!"

She couldn't stand his arrogance, not one bit and as she made her way to the control room again to check in with her front line team, her concern was evident by the way she reacted to the conversation that took place.

"How is Major Sheppard?" Elizabeth asked, looking into the event horizon as if she would see them.

"I'm still here." John replied, and Elizabeth could almost feel him grimacing in pain.

"Hang in there Major. We're working on the problem."

"I know you are. Listen- uh- I'd like to say something while I still can."

"DON'T!" Elizabeth ordered, her heart constricting at the thought of John leaving her. "You're going to get through this." He kept talking, something about the Wraith leaving him there and Elizabeth only clued into what John was leading up to when he cleared his throat.

"What I wanted to say was…"

"Save your strength John, and tell me in person." Elizabeth whispered.

"This is important."

"I'm listening."

But she didn't have to hear what John was going to say because her team figured out a solution. She didn't like it but it was John's best chance at survival and she waited with baited breath while they shocked him and when Ford replied that he they couldn't revive John her heart fell to the floor and she only hoped that Beckett would be able to save him. Then the waiting game started and she found herself telling Rodney to just pick a pathway at random and then after another couple of moments the Puddle Jumper appeared and rose to the Jumper bay. Elizabeth ran in and found McKay standing near the exit looking at Ford. "He's going to be fine." Elizabeth took Ford's hand for a moment, thanking him for what he was done and then turned her attention to John, who's heart was flat lining. She felt like she was on auto pilot and found herself turning to Rodney and telling him well done and she only barely heard him say "We'll see" Her attention was back on John with the medic pumping air into him and then, to her own heart's relief, the monitor began to beep regularly

"We've got a pulse…..Getting Stronger….. He's going to be OK."

Elizabeth heard Rodney sigh in relief and she herself felt like her legs would no longer support her and she sank to the bench and placed her hands to her face in the prayer position, thanking what ever divine being saved him.

Later, she was able to see him, and she asked him what he was going to say, and he told her- sort of.

"I was going to say, um………………take care if each other."

"That's nice"

"Yep."

"And- uh- indeed we did."

"Yes. You did. Thank you. _Again!"_

"You're welcome."

"Good night."

"You weren't really going to say that, were you?"

"I have no idea what you're talking about."

"I didn't think so."

It was months later, during the largest storm that she had ever witnessed when they had just about had Kolya fooled when John was still in the hallway and there was the possibility that he would be electrocuted. She tired to stall, but it didn't work.

Minutes later she was being pulled towards the event horizon when John came into View. He and Kolya exchanged words and she just looked at him panicking. She was going to loose him, she knew it- she thought that he wouldn't risk firing on her, but he did, and she found that she was still with him.

It was later, during the siege, and she was about to give the order to evacuate when….

"Elizabeth wait!" He was stopped halfway up the stairs and he turned to look at her. Elizabeth turned to face him and in horror, she realised what he was going to do.

"You can't" She pleaded as if her own words alone could change his mind. She didn't want to loose him, after so many close calls, she knew that if she let him go she would not see him again. He, who and come to mean so much to her, he who had saved her and Atlantis countless times, he who-

"I have to…" John stated, not wanting to do this either, but he wanted to keep her safe. "…and you know it."

"John," Elizabeth protested shaking her head…there was so much that she wanted to tell him, so much she wanted to share and as the moments passes and they stared at each other she realised that this was one negotiation that she would not be able to get out of. She knew in her heart that his plan was the bets way to save Atlantis and that she would have to let him go. "Go." With a sinking heart, she watched as John nodded and raced up the stairs. With all her strength forcing her self not to cry or to run after him she closed her eyes and bowed her head in an attempt to gather strength.

When Colonel Everett asked her the status of the Jumper, she could barely speak and yet she did. "It's on its way." And when Zelenka radioed that John was indeed taking the jumper out she wanted to tell Zelenka to stop him, but she knew that she couldn't and she radioed him back. "I'm aware of that Doctor Zelenka- start prepping Jumper Two." She had the gene therapy, and she had a basic knowledge of the Jumper, she would take the second one out. When Rodney stated that they had to evacuate she found her resolve grim and determined. "We're not going anywhere- not yet." 'Not until we see if John's plan work. We are not going to leave and let him die for an empty city."

"You know," John radioed in. "If this works, somebody might have to do it again."

"Understood." And she did understand, she would do it, she would not put anyone else's life in danger.

When Rodney finally figured it out, Elizabeth couldn't answer and ordered that they arm the self-destruct in case John's plan failed…and then he radioed in that he was going into the hive and Elizabeth couldn't watch the screen but she knew that his plan was successful when a bright light flashed in the sky and though Atlantis. A technician said that the target had been neutralised. And after bowing her head in respect she, with tears in her voice said "He did it." He was gone, he was real and truly gone and then her grief turned to panic when another ship approached, and then her panic turned to shock and relief when she heard…

"Atlantis, this is Sheppard."

"John!"

"What other Sheppard's do you know?"

Then, once the other hive ship had been destroyed, and the shield was up, he beamed down and once she saw him she just couldn't resist her feelings, she had been on edge for to long and she wrapped her arms around him and embraced him in a huge hug.

Nearly a month later, she almost lost him again, he was speeding away in a defective jumper and her lying was more to herself then it was to him. After all they had been through, she couldn't believe that she was going to loose him to a damn Wraith computer virus

Then, he disappeared with out a trace, he didn't check in- no one could figure out where he had gotten too and as she ordered the rescue teams, she kept hoping that he would be able to make it out of where ever he was on his own.

When the pictures were placed in front of her, she couldn't believe it- he had been targeted and now she had lost contact with him and she didn't know if she would ever see him again. Then she found out that it was Genii and she found herself bargaining for John's life. Cowen wanted 10 jumpers, they would be crippled with out them- and she only had 15 minutes. But she could save their people and she tried but Cowen still said that he was going to kill John, and then- there was nothing but static and she tried frantically to think of a plan- but nothing came to her…. Luckily the coup was real, and John came though the gate safe and sound.

He was stuck on the other side of a time barrier, where time was flying by and she could only hope that they rescued him before he died of old age. 'Dying of old age-' Elizabeth thought to herself in horror as she stepped through the gate to save him. 'Don't worry John, you saved me plenty of time, now it's my turn.'

He was turning into a Wraith, and she was loosing him. Each time she went to see him, she could feel it. Little by little John Sheppard was slipping away from her and turning into the very thing that she despised. She tried to comfort him, but even he knew that there was little she could do. And while her mind searched for a way to save him, her heart tried to find the words that she wanted so desperately to say.

She was ordering Teyla to kill him, she was screaming for Teyla to stop but Teyla couldn't hear her. Phoebes had taken control of her body and she was going to watch as the man she depended on so much died, by her orders. She prayed that something would stop Teyla, but as the seconds counted down and she actually raised her weapon to John Elizabeth's heart broke, knowing that she- or at least her body will have given the order to kill the man whom she loved.

When they came through the gate, and the shield was raised behind her, she knew that something was deadly wrong. And when she realised that they could not get a lock and that the gate had probably been swallowed by the magma, her mind raced to find a solution and once again she prayed that she would see John, her John alive.

There was something wrong from the very beginning, she knew that if she answered the Wraith that something would unravel that she would not be able to control, and she had been right- and now as Zelenka told her that it had been a trick all along- her mind went to John, and wondered, hoped and prayed that he was alright and had not done something stupid and heroic like he always did.

end of flashbacks

"I tend to do that a lot, don't I?" John asked with a weak laugh as he tried to process all the emotion that had flooded to him, from Elizabeth in the last few seconds.

"Yes." Elizabeth replied with a small smile breaking the hug and looking into his eyes. 'And every time I died a little inside.'

'Elizabeth.' John thought, letting her know that they were still connected

'Oh god.' She thought in horror as her feelings rose to the surface. "We're still connected."

"Apparently," John replied after which he coughed and a little blood appeared at the corner of his mouth causing Elizabeth to have a hard time controlling her thoughts and emotions.

'Oh god John, don't you dare die on me now. Not now- not like this.'

"I am not going to die on you." John replied out loud trying to show her that he was strong.

"Of course your not," Elizabeth confirmed trying to be strong herself, but even she knew deep down that he probably had pretty severe internal bleeding.

"Elizabeth…." John muttered after a coughing fit and his body seizing up in pain. "I need….I need to tell you something…"

"No John," Elizabeth ordered doing her best to not listen to his thoughts and blocking her own from him. "You don't have to tell me anything, because you are going to get though this."

"Elizabeth…" John muttered again and Elizabeth looked up at him and her heart nearly broke at the look of his face. She had never seen him so defeated and it scared her. "Elizabeth…wh-what did you mean when you said that you died a little inside…."

"Oh John I…." Elizabeth was going to think up of some excuse but after pausing for a moment she looked up again and found that John was slipping away from her. Not only could she see it in front of her eyes but she could feel it in her mind and heart. "John? John, wake up. John stay with me John!" Unable to help herself Elizabeth closed the small gap between them and kissed John on the lips, attempting to keep him in the land of the living. It was only when she felt him kiss her back and when his arms went around her as well that she broke the kiss, pulled away and looked down as if in shame.

"Elizabeth what-" John asked and when Elizabeth looked at him he didn't need to hear the answer from her mouth or her mind, he could feel it in his heart. "Oh,"

"I'm sorry John," Elizabeth apologized thinking that the shock on his face meant that he didn't feel for her the way she felt for him. "I shouldn't have done anything- you were slipping away and I didn't- I couldn't- I-"

"I never knew." John stated weakly. "I-"

"You weren't supposed too." Elizabeth answered moving back a bit. "You don't-"

"Elizabeth I-" John began as he took her hand and she was plunged into his memories as he was plunged into hers.

flashbacks

He was dying, he knew it. That damn bug was sucking the life from him and the only thing he wanted to say was how much he appreciated working with her and how he hoped that she would be strong with out him and she wasn't letting him speak. He wanted to get back to her, to protect her, but he didn't think that he could

It was the storm of the century, and Atlantis had been attacked in its weakest moment and as he went around trying to figure out a plan and disabling what he could he was contacted by Kolya with the most horrible news.

"Say good bye to Doctor Weir."

'NO!' John thought frantically and it was all he could do but yell into the radio and yell his name, as if that would stop him "Kolya! KOLYA! KOLYA! Don't do this!"

There was silence and John's heart was beating frantically. 'Can't loose her, not now, not like this.' And as he waited he didn't dare to move, as if by moving Koyla would actually kill her, 'But he can't, he needs her. He needs her, he-"

"Major Sheppard…" Kolya spoke into the radio stopping John's thought in mid-sentence. "How's this for credibility? Weir is dead."

'NO!' His mind screamed and he wanted to scream at Kolya too, but he wouldn't give that bastard the pleasure. He took a very deep breath to calm him voice and then slowly as he pronounced each word he gave Kolya his threat. "I. Am. Going. To. Kill. You."

Everything he was doing, he was doing for her. Disabling the generators, stopping from their men by putting up the shield, all of it was in revenge for her. He may have lost her, but he was going to make sure that Kolya would feel what he was feeling. That was when he was contacted again over radio.

"Major Sheppard, I have a proposition for you."

"Kolya, I'm having a hard time keeping up…" John gloated. "What's the score again?

"My men have informed that not only have you disabled some crucial generators….you've stolen key components that make it impossible to be restored."

"Yeah," John confirmed feeling a small bit of satisfaction. "I did that." 'For Elizabeth.'

"There are two flaws in your plan."

"Always open to constructive criticism." John taunted.

"One, the assumption that I would believe you would rather destroy the city than let it fall to us is childish."

"Doesn't sound like me." John replied.

"Second, if and when I determine Atlantis unsalvageable, Doctors Weir and McKay become obsolete."

That stopped John walking down the steps, and after a couple of moments of calming his breath he spoke. "……..Weir's alive?"

"Doctor McKay was able to make a strong case for keeping her alive…"

"Let me talk to her." John ordered, almost desperately and he waited for what seemed an eternity till she answered.

"Sheppard, we're both here!" She yelled over the force of the storm.

"It's good to hear you're voice." John replied, his voice oozing relief.

"Yeah, it's good to hear." Elizabeth agreed and then John heard Kolya saying that he had 10 minutes to fix grounding station 3 or else Elizabeth would die.

"Again you mean?" John asked fearfully but doubting that he would kill her because he still needed her.

"Her death will…" John barely heard the rest and when Kolya was finished he realised that the time that he had been given wasn't enough and when Kolya let him know that he was serious he ran trying to save her…again.

He had succeeded, and when he and his team finally made it to the gate room, he found that he was about to loose her to Kolya through the gate.

"You're not going anywhere." John stated out loud as Kolya edged closer to the event horizon with Weir. "I will shoot you if you don't let her go."

"And risk hurting Dr. Weir?" Kolya asked, not buying the thread.

"I'm not aiming at her." John stated after standing and he fired a single shot and Elizabeth fell to the floor and he ran over to her and apologised. "Sorry about that I had to ermm…" He stopped realising that she looked very shaken up. "You okay?"

"uh- no." Elizabeth replied shaking her head.

"You will be." John promised. "Come on." And he took her hand and together they ran up the steps to the control room to save their city

It was later, during the siege, and she was about to give the order to evacuate when….

"Elizabeth wait!" He was stopped halfway up the stairs and he turned to look at her. He couldn't leave her without saying goodbye. And as he looked at her, he almost changed his mind when he saw her face.

"You can't" She pleaded as if her own words alone could change his mind.

"I have to…" John stated, not wanting to do this either, but he wanted to keep her safe. It was all he could do, he had to keep her safe and he had to convince her that letting him go was going to be the only way. "…and you know it."

"John," Elizabeth protested shaking her head… and in that moment he just stared at her, trying to tell her with out words that he cared what happened to her and that to save her and Atlantis this was the only way. He tried to tell her that giving up his life would not be the worst thing, loosing her was by far the worst thing he knew that he would have to deal with and that she had to let him do his duty. "Go." Elizabeth replied and with a nod he ran up the stares feeling her eyes in his back, pleading with him to come back and he wanted to, he really did but his sense of duty was driving him. His protective instinct was driving him to save her the only way he knew how.

Zelenka radioed that he was taking the jumper and he heard her tell Zelenka that she knew and that he had to prep Jumper two. At the sound of his voice he again almost changed his mind but he knew that he had to do this, so he took the jumper up and aimed it right down the throat of the hive ship. After a couple of minutes he suddenly thought of something and wondered what Elizabeth was going to do about it.

"You know," John radioed in, his own voice not near as calm as he wanted it to be. "If this works, somebody might have to do it again."

"Understood." Elizabeth radioed back and he wondered what that tone in her voice was. 'What is she going to do?'

Minutes later, he was saved, and after the first hive ship was destroyed he thought that he better radio in that he was alright.

"Atlantis, this is Sheppard."

"John!" Elizabeth radioed back in shock.

"What other Sheppard's do you know?"

Minutes later after the second hive had been destroyed John realised that Atlantis had a huge problem.

"Elizabeth, you've got a problem."

"We see that, Major."

"We're moving to intercept but I don't think we can get there in time."

There was chatter and John realised that he was going to loose her again if Rodney didn't get that shield up. "You'd better get the damned shield up!" He ordered frantically and he waited. And once the darts were clearly there he tried to radio Atlantis.

"Atlantis, this is Sheppard, come in." There was silence. "Atlantis….Elizabeth….I repeat. This. Is. Sheppard. What is your status?"

"We're still here." Came Elizabeth's reply. "That's our status."

"Don't scare me like that!" John pleaded after a sigh of relief.

Caldwell offered him a change to go back to Atlantis and he was beamed down. Once he was oriented, which took a couple of seconds he ordered the marines who had beamed down with him to secure Stargate operations. He then saw Elizabeth coming down the steps to meet him and he stated, rather clichéd that he was home. To his great surprise, Elizabeth walked to him and then after a moment she wrapped her arms around him and pulled him into a hug. After a moment of shock, John reciprocated the hug and embraced her back. His hesitation was not because he wasn't relieved to see her, he just t embraced him in a huge hug.

Nearly a month later, he almost lost her. He was speeding away into space in a defective jumper. He knew that she was lying to him and he tried to remain positive. After all they had been through with the Wraith, he didn't want to leave her like this- luckily he didn't have too.

He was turning into a Wraith, and she was loosing him. Each time she went to see him, she could feel it, he knew that she could. He was changing, he was scared and little by little the John Sheppard that he knew was slipping away. He was turning into the very thing that they both hated and if this went to far, he wouldn't be able to communicate at all. He told her to stay away from him, but she didn't listen and as he realised that he was holding her by the throat he realised that he had to get away, before it was too late.

Ford had kidnapped him as his team and they were missing for a long time while McKay tried to implement Aiden's plan. All the time that it took, he thought of Elizabeth and tried to find a way to get back to her. He was not going to let her think that he had abandoned her- or worse that he was dead. He was going to get back to her. He was.

He was stuck, he couldn't get back to the other side and he waited a long time and his team only sent little supplies though. He left the cave to look for shelter and there he lived for months. Each day the hurt burying deeper and deeper, they had left him behind. She had left him behind. For months he tried to fit in, but the people he was with were not the same as the people of Atlantis. Even the girl, was not the same as Elizabeth and when she told him that they were near and that the beast was after them, he went to save them- even though she had taken so long to find him.

Phoebes was ordering Teyla to kill him. He didn't think that Teyla was going to do it. They had much to deep a respect to do it. When Thalen told Teyla a version of this, he couldn't help but cringe. He and Teyla had a respect, and he cared for her as a friend, companion and warrior but nothing more. He cared much deeper for someone else and he couldn't believe that he was hearing her voice order Teyla to kill him. He was going to leave her without ever telling her how he felt. He was screaming, screaming for her to hear her. But it was no use.

He had been taken by the Genii, he couldn't believe it. And his life was being bargained for jumpers. He knew that she was never going to give in, and yet while his mind tried to figure out a plan- he thought about how she was handling it- and if Cowen would actually kill him.

The volcano was exploding, and he didn't know that he would survive it. With the gate buried in lava and the Dedalaus still away, John could only hope that he would get out of his situation. All he could do is pray that they made it out of the bowls of the Ancients science station alive. There was just too much at stake, the Wraith were coming- and he had to be there to protect her. He just had to be.

end of flashbacks

"-do." John finished, slightly shocked as he released her hand. The link between them was clearly growing stronger and Elizabeth just looked at her hand for a moment and then looked at him with wonder in her eyes.

"John," She whispered her voice soft yet secure. "Why did you never tell me that you felt the same?"

"Well, at first there was Simon…"

_I met someone else…_

"Simon left me a long time ago John." Elizabeth whispered, shaking away the memory of his rejection. At the time, she had been hurt- but not because she loved Simon that much but because she thought that she could trust him- but Elizabeth had already learned to trust someone else.

"I know." John nodded his head weakly. "But I thought that you-"

"Still carried a torch for him?" Elizabeth asked turning to John who nodded his head. "No, I left him back on Earth John….. I was just afraid before. I didn't want to get hurt again."

"I swear to you Elizabeth." John stated reaching out his hand and placing it lovingly on her cheek. "I will never hurt you."

"I know that." Elizabeth nodded, a small smile on her face. "But we can't-"

"Oh my god." Came a familiar voice behind them.

"Carson?" John asked weakly and Elizabeth turned around to see the gang. Rodney, Zelenka, Teyla, Ronan, Aiden, Carson and several Athosians behind them

"What happened to the Colonel?" He asked running over to John, his doctor instincts kicking in.

"Got into a shooting match with a couple of Wraith." John muttered weakly.

"And it looks like you lost." Rodney stated, his anxiety sounding like giddiness.

"Rodney for heavens sake," Carson chastised Rodney before turning back to his patient. "Now Colonel Sheppard, we have to get you to the Infirmary."

"No."

"No?" Carson asked looking confused.

"We- we have too…" John stuttered trying to make his point known and he turned his head to Elizabeth who had been crouching on John's left side to finish the sentence. After a second or too, she nodded and stood facing her team.

"We have to save Atlantis first."

"What?" Rodney asked out loud. "How?"

"Ch-Chair?"

"What?" Rodney asked again pointing to Sheppard. "What did he say?"

"I believe that he said chair?" Zelenka asked looking to Elizabeth for confirmation and Rodney snapped his hands together in amazement.

"Your brilliant." Rodney remarked to John, who was fighting to stay conscious. "You know that right?"

"What are you talking about Rodney?" Carson asked not understanding.

"Sheppard's going to power the chair, use the hive drones and destroy the hive ship."

"Now that's a plan." Ronan approved.

"Indeed." Teyla agreed.

"And because the chair needs the gene to work," Zelenka began with a smile on his face. "It means that it won't have been locked down like the rest of the systems."

"So now all we have to do is get to the chair room." Rodney pointed out.

"I'm sorry." Carson interrupted. "But Colonel Sheppard is not going anywhere, let alone operating that damn thing. He probably has a concussion, a severe wound to his shoulder and he probably has internal bleeding. I have to get him to the infirmary."

'No!' John cried out weakly to Elizabeth. 'No, you can't let him to this! I- I have to save Atlantis.'

'We can save Atlantis with out you John,' Elizabeth thought as she knelt beside her fallen soldier, ignoring the questions and arguments of the others.

'No.' John argued, his mental voice getting weak. 'I- I have to save me.'

'You've saved me enough times John.'

'O-one last time then.'

"No!" Elizabeth cried out loud, bringing all the focus onto her. After a split second of embarrassment Elizabeth composed herself and turned to Carson. "Carson, I know that you are the doctor but this is one instance where I have to over ride your authority."

"But-"

"Carson, John is dying." Elizabeth snapped, trying to keep control. "He doesn't have time and if he- if we can't get to the chair in time we will all follow. We need to go now."

"Very well." Carson replied with a resigned sigh. "But we will have to hurry."

"Don't worry." Ronan replied helping Elizabeth get John to his feet. "If we are too slow, it won't matter for us now, will it?"

"No." Elizabeth confirmed shaking her head. "Now, lets save Atlantis…shall we?"

Meanwhile back in space, out side the Wraith armada's sensors both the Dedalaus and the Orion were waiting.

"Caldwell to Lorne, do you read me?" Caldwell called the commander of the Orion for this mission.

"Loud and clear sir," Lorne answered.

"Any word from Atlantis?" Caldwell asked, hoping that the Orion's sensors would have picked something up that he had missed.

"No sir." Lorne replied. "However, our sensors are detecting many life forms in the chair room- if it is our people…."

"Then we should be in for one hell of a light show." Caldwell finished. "Good work Major Lorne."

They all arrived in the chair room. The Athosians, along with Ronan, Teyla created a perimeter while Rodney and Zelenka made sure that all the chairs systems were functioning properly. While this was going on, John was being lowered into the chair by Elizabeth and Carson.

"I still don't think that this is a good idea Elizabeth." Carson stated. "Sheppard is in too weak a state right now, I don't think that he will be able to operate the chair."

"Then you can do it." Elizabeth replied distantly as she took John's hand in her own. 'John, hang in there.'

'I'm trying.' John thought back, his mind weak.

"No." Carson stated shaking his head. "No way, I'm just saying that I can't operate this thing on the best of days, there is no way that I would be able to do it now."

"Then we let John do what he has been trained to do." Elizabeth sated, her voice cold and strained. "Rodney, Zelenka- are you almost finished?"

"Yes." Zelenka agreed.

"The chair, thank god, has remained undamaged by our little lockdown virus. Sheppard should be able to power it up." Rodney finished.

"Do you hear that John?" Elizabeth asked turning to John. 'It's your turn to save the day.'

'Elizabeth…' John whispered as the chair lit up and Elizabeth found that she had to back away while the chair rotated.

Suddenly there was gun fire, and the sound of wraith stunners. The Athosians, Ronan, Teyla, Carson, Rodney and Zelenka all dove for cover but Elizabeth was too shocked to do anything. She just stood there frozen, looking at John who was looking at her and in a moment, she thought that she was dead. She turned and saw the Wraith firing a P-90 at her, yet the bullets didn't hit her. They hit a purple force field that suddenly sprang up.

"The chair has a shield?" Rodney asked coming out of hiding.

"Apparently." Ronan stated looking face to face with a Wraith who was banging his hands on the shield. "A good one too."

"He saved your life Elizabeth." Rodney pointed out, pointing to John.

"Elizabeth…" John muttered.

"I'm here." Elizabeth answered kneeling beside the chair, placing her hand over his left one- the one that wasn't controlling the chair. 'Thank you for saving me.'

"I will always save you…" John whispered turning his head to Elizabeth and then the chair disengaged and John fell completely conscious.

"John? John!" Elizabeth cried standing up to look at his face, but in the process- she too felt nauseated and she fainted to the ground.

"Great." Rodney muttered watching as Teyla went to check on John as Carson monitored Elizabeth.

"Did he do it?" Ronan asked looking around. "Did he get the ships?"

"Rodney." Zelenka began but Rodney cut him off.

"I-" Rodney began when suddenly large explosions could be heard.

'Rodney." Zelenka began again but once again Rodney cut him off.

"I think he did." Rodney stated proudly.

"Rodney!" Zelenka yelled.

"What?" Rodney asked turning to his fellow scientist. But Zelenka didn't have to tell him, Rodney's eyes just went wide in terror and in a flash he was out of the room.

"What was that all about?" Ronan asked.

"The shield, it will need to be up." Zelenka explained. "With out it, the pieces of the Wraith ships have a high probability of falling into Atlantis."

"We better help him then." Ronan stated running off, motioning for half the Athosians to follow with Aiden close behind. Teyla and the rest stayed behind and guard Zelenka, Carson and their fallen leaders.

Meanwhile up aboard the Dedalaus and Orion, cheers erupted as they saw bright flashes across their sensors. The location of the flashed indicated to all that indeed, the Wraith had been destroyed and that once again Atlantis was safe from harm and invasion.

"Novak to Caldwell?"

"Yes Novak?" Caldwell answered over the comm. Link

"Uh- Sir, Hermoid predicts that unless Dr. McKay was able to get the shield up on time, Atlantis- well it would have been destroyed by the falling Wraith ships.

"Sir-" Major Lorne stated over the ship to ship communications channel. "We have a hundreds of hostiles, incoming."

"It is probably just the darts leaving-" Caldwell predicted. "Stay where you are and wait, do not engage the enemy unless they engage you, understood?"

"Yes sir."

"Now, Novak, what were you saying?"

"Dr. Novak was relating the fact that unless Dr. McKay got the shield up, the debris from the hive ships and wraith Cruisers would have destroyed Atlantis." Hermoid answered in his straight and un-feeling tone. There was silence across the bridge of the Dedalaus and eventually across both ships as the realisation of what might have happened began to sink in.

"Well, let's just hope that didn't happen." Caldwell stated after a few moments. He waited a couple of more seconds and then he addressed his helmswomen. "Lieutenant- Are there any more hostiles incoming?"

"No sir." The female Lieutenant answered. "The explosions of the hive ships are blocking our sensors, but from what I have been reading, it looks like no more darts are coming from that area that Atlantis is supposed to occupy."

"Can you get a read out on whether Atlantis is still there?"

"No, sir- I cannot."

"Then take us in Lieutenant." Caldwell ordered.

"Yes, sir!"

"Major Lorne?" Caldwell asked, contacting the other ship.

"Yes Colonel?"

"We're going in, assume that there are hostiles in the city if it is still standing."

"Yes sir."

All communication between the ships fell silent as they approached the planet to get a visual on the city. As they drew closer, and their sensors began to clear up and they soon realised that they would be able to get a reading on if the city was destroyed or if it was still standing. The ships dipped below the cloud line and a sigh of relief swept through the ship as they saw that Atlantis was indeed still standing. The only question that remained un answered at this point was if the personal were still alive.

"Atlantis. This is Colonel Caldwell. Come in Atlantis." They had a visual, the city was standing. The shield must have been in place when the chair was activated and Caldwell just prayed that the expedition members survived. "Atlantis, this is Colonel Caldwell. If anyone is reading this transmission please respond." The line crackled for a moment and then there was a response.

"Colonel, this is Teyla." Another sigh of relief swept through the bridge crew.

"Teyla," Caldwell responded, relief evident in his voice. If she had survived, the rest of the senior staff probably survived as well. "It is good to hear your voice!"

"There can be pleasantries later Colonel, but first I insist that you transport Colonel Sheppard and Dr. Weir to the infirmary along with Dr. Becket."

"Why?" Caldwell asked, the fear starting to rise again. "What happened?"

"Colonel," Carson interrupted. "I have two patients who are dying here in the chair room- so please stop asking questions and transport us and some of your med people to my infirmary."

"Yes of course, but the shield will have to be down for us to do anything." Caldwell answered after a Lieutenant whispered in his ear.

"RODNEY!" Carson yelled through the city communicator.

"Yes, yes." Rodney replied. "I heard, shield down….now."

"Please Colonel." Teyla pleaded through the transmission. "Now." There was a flash of bright light and Teyla found herself alone in the chair room. "Thank you." She replied to Caldwell. "You an the Orion can dock on your respective piers. East and North- we desperately need your help to exterminate the remainder of the Wraith who are still in this city."

"Right away Teyla." Caldwell replied, preparing to do another clean up job.

It was hours later- all the Wraith had been eradicated from Atlantis and the med personal had gathered enough enzyme to ensure that Aiden's remaining de-toxing period would be as smooth and as painless as humanly possible. And hours later, all the remaining senior staff, with the exception of Carson, Elizabeth and John were stood over the beds in the surgical room and watched as Carson operated on John.

John, to everyone's dismay had sustained several serious injuries as a result of his battle with the Wraith. He had a few cracked ribs which had punctured a lung, a severe concussions, a large gash at his hairline and a bullet through his shoulder. Normally, Carson would have been seriously worried at the amount of damage that his patient had taken but the fact that John had used his remaining energy up with his heroics in the chair room worried him even further.

It seemed that he was slipping away and every so often Carson took his eyes away from John to look towards his other patient Elizabeth and trying to gage John's vitals by how well Elizabeth was doing.

The sun was setting and the golden light bounced off their faces as they stood on their balcony overlooking the piers of Atlantis, the sea and the horizon. Their world was idyllic and peaceful and neither of them wanted to break the silence for they were both lost in their own worlds. It was when Elizabeth felt a presence beside her that she broke the silence.

"John?" Elizabeth asked, feeling the presence of someone beside her.

"Elizabeth!" John replied shock emanating from his voice while his body and face was looking as healthy as ever. "I did it didn't I?"

"Did you?" Elizabeth asked, the memories of what had transpired in the chair room. :I don't really remember- it's so fuzzy. You collapsed and then I, I-"

"Fainted," John finished, as he himself remembered what had happened. "Yeah, I was vaguely aware of that….but I defiantly remember sending a drone to each of the hive ships, and most of the cruisers as well. I know that there is no way anything bigger than a dart could have survived our attack in fact-" John paused as if lost in his own thoughts. "Carson, Carson is-"

"Operating on you." Elizabeth finished feeling John's life slipping away from her and she didn't know if it was the link dissipating or if he really was dying. "Oh God John!" She exclaimed taking John by the hand. "You're slipping away from me, I can feel it I-"

"Shhh," John soothed placing his other hand over Elizabeth's. "It's alright."

"No." Elizabeth replied shaking her head watching in horror. "I can see it now. John, you're fading," John took his hands back and put them in front of his face and saw that he was indeed fading. "You're fading away from me, John. You can't leave me. Not now, not like this!"

"Elizabeth…" John stated, his voice starting to have a hint of worry in it as he faded away more. He put his hand out to touch Elizabeth's face but his hand went right though it.

"No, John-" Elizabeth pleaded. "No, you can't leave me!"

"Elizabeth-" His voice was more frantic, he was almost completely translucent and his panic made Elizabeth's grow tenfold.

"You said that you'd never hurt me." Elizabeth cried, tears falling down her face as John faded from her sight bit by bit. "You said, you swore…"

"Elizabeth- I love you."

"John I-" Elizabeth began but she never got to finish her sentence. He was gone, vanished before her very eyes and as the realization sunk in, and the horror at not being able to feel his presence any more was understood by her mind and her broken heart, her idyllic world crumbled around her and she screamed. "NO!"

"John!" Elizabeth cried sitting up in a medical bed. At first disorientation struck her, 'Wasn't I on the balcony?' but then she heard Carson's voice calling her and she turned to look at him.

"Elizabeth?" Carson asked again as he left the nurses and surgeons to finish up the operation on John. "What happened?"

"I don't know." Elizabeth answered honestly as she placed a hand to her head which felt so empty with out the constant stream of John's thoughts. "John and I were linked and then he- he disappeared. Vanished- Oh god Carson, he's not-?"

"No." Carson interrupted with a shake of his head, watching as Elizabeth's eyes closed and a sigh flow from her body and he knew that he had to tell her what had happened during the operation. "No. He's not dead, thank heavens. But he is extremely weak and unfortunately the medically induced coma that I put him in for the operation may have taken a more permanent effect."

"What!" Elizabeth cried out in horror. "How could-"

"I am very positive that, that is not the case Elizabeth but we will just have to wait and give it time."

"Time? Time? Carson how in the world could you have done this…?"

"Wow," Ronan remarked watching as Elizabeth's body language showed that she was most upset at the doctor. "She's upset."

"You're telling me." Rodney agreed. "I don't think I've ever seen her that upset."

"Colonel Sheppard is in a coma." Teyla interrupted trying to give the boys a women's perspective. "He and Dr. Weir have been linked for the past twelve hours, such things do not happen without the people involved getting-close. I would not be surprised if they were able to work through many things- most of which hinge on Colonel Sheppard getting better."

"What?" Rodney asked looking from Elizabeth, who was still yelling at Carson to Teyla. "What are you talking about."

"Have you not seen it?" Teyla asked, shocked that they had noticed it. "Have you not felt it? The way they look at each other? How close they are together both physically and mentally? Have you been blind to the feelings that they both share for each other and the absolute worry and despair that they both go through when the other is in trouble."

"Teyla, what are you talking about?" Caldwell asked stepping forward, even though he had an idea of what she was saying.

"What I am saying Colonel Caldwell is that Dr. Weir and Colonel Sheppard are in love."

"With each other?" Rodney asked shocked.

"Are you blind McKay?" Ronan agreeing with Teyla, "Think of all the times when they have been separated from each other."

"Well I always knew that they were close but…. oh my god." Rodney muttered. "You're right."

"Of course I am right." Teyla answered back. "So let us hope, for Doctor Weir's sake that John gets better soon."

"A happy leader is a strong leader." Caldwell muttered, reciting something an admiral had told him a long time ago.

"What?" Rodney asked, not catching what he had said.

"A happy leader is a strong leader."

"Indeed." Teyla agreed turning her attention back to Elizabeth who had finally settled down. 'I pray to the ancestors for you Dr. Weir. May he whom you love return to you, and make you happy. You are both stronger together.'

It was three days after the Battle for Atlantis, Carson had tried giving John a number of stimulants to break him out of the coma that he had slipped into however none of them were working. Caldwell and Major Lorne had taken over the day to day operations of Atlantis while their leader kept a constant vigil over John Sheppard.

Not one of the Atlantis expedition members questioned her choice. They all knew what Shepard and Weir had been through together in the past few years and since their two leaders had just been linked together for twelve hours, they all knew not to ask questions or to bother her unless it was an emergency and fortunately nothing tragic had happened to that point.

"You should get some sleep lass," Carson suggested as he was preparing to leave the infirmary for the night.

"I've slept Carson." Elizabeth whispered though her hands which were to her face. "I have slept."

"A couple of hours each night for three days straight will not do your body any good Elizabeth."

"You know what Carson, I don't really care." Elizabeth argued. "I can't leave him. Not after all he's done."

"Elizabeth…."

"Goodnight Carson." Elizabeth stated and there was such a finality to her tone that Carson didn't dare to argue with. Therefore with a sigh, he left and after several moments of silence with Elizabeth just staring at John's sleeping form she spoke up, trying to brightly cover up her emotions. "John? John you did it. You saved Atlantis, the Wraith were destroyed, and they don't seem to be coming back. John?" Elizabeth paused to take John's hand in her own. "John, you saved me." She whispered her voice softening and her true emotions coming to the surface. "John, you said that you would never hurt me. John you swore that you would never hurt me and you are hurting me. John please wake up." Elizabeth pleaded, tears coming to her eyes and small sobs interrupting her speech. "You're hurting me. You're hurting me John and you swore that you wouldn't. Oh, John, p-please wake up. Please John. Please." Elizabeth sobbed. 'You're hurting me John, please wake up and make the pain go away.' Her mind echoed.

'I'll never hurt you.' John's voice floated though her head.

"John?" Elizabeth asked out loud, her tears stopping in surprise at hearing John's voice/ "John?" She asked again staring at him however after what seemed like an eternity she realised that she must have been imaging his voi9ce. 'Oh John,' She sighed in her head, tears coming to her eyes again.

'Elizabeth?' His voice was soft, distant and confused yet it was strong at the same time, as if it was looking/ searching for something.

"Ok, this time I know I heard something." Elizabeth muttered looking around when all of a sudden from the corner of her eye she saw a little bit of movement. "John?" She asked thinking as if she was loosing her mind and when John moved again and she saw that he seemed to be in a nightmare. 'Oh having a seizure….oh god…' "CARSON!" Elizabeth called into her communicator.

"What is it Elizabeth?" Carson asked his voice sounding tiered and weak through the communications channel.

'Elizabeth?' John's voice echoed through her head.

"John?" Elizabeth asked leaning over the bed.

"Elizabeth?" John moaned out his eyes fluttering.

"Elizabeth?" Carson asked through the communications channel. "Is everything-"

"He's awake!" Elizabeth shrieked with joy. "Carson, he's awake!"

"Alright, I'll be right down."

"Of course I am awake." John muttered opening his eyes further. "Why wouldn't I be?"

"Well-"

"Good heaven's colonel." Carson replied entering the room and interrupting Elizabeth who sank into her seat and took John's hand in her own. "You gave us all quite a scare."

"Scare?" John asked pulling himself to a sitting position while Carson checked all of his vitals. "What do you mean, scare…Elizabeth what is going on here? I heard you calling my name- or something directed towards me I don't really remember and then-"

"Pardon?" Elizabeth asked taking her hand away. "You heard me talking to you?"

"No." John replied as if that was the most ridiculous thing that she had ever said and that he had ever heard. "I heard you- up here." He answered tapping his head to indicate that it was not through his ears that he heard her but through her mind.

"But the link…" Carson muttered re-checking his vitals.

"Carson, you said that we lost the link three days ago, twelve hours after it had bonded us together in the first place."

"Three days?" John asked, not understanding the three days comment. "Would someone please tell me what is going on?"

"John," Elizabeth began softly taking his hand again. "You've been in a coma for three days."

"Three days? That can't be right! I was in the chair, hours have passed maybe but days and… Elizabeth. The Wraith?"

"Totally defeated Colonel," Carson interjected. "With no sign of returning."

"Really?" John asked turning from Carson to Elizabeth with a smile on his face. "You mean I did it?"

"Yes," Elizabeth replied her voice soft and her eyes misting up with tears. "You were quite the hero back there."

"Uh, Carson, could you leave us alone?" John asked turning to Carson. "We, have a lot to talk about."

"Oh, very well Colonel." Carson sighed. "Your vitals are normal, and I suppose that you've had enough sleep over the last couple days- heaven knows that I haven't- so if you'll both excuse me, I am going to bed….and you should think of doing the same Elizabeth."

"What do you mean Carson?" John asked looking concerned.

"It's nothing." Elizabeth interjected.

"It is certainly not nothing lass…" Carson interrupted. "She's been keeping a constant vigil at your side Colonel…she's hardly slept herself."

"Well then, I won't keep her long." John promised. "Thank you and goodnight Carson."

"Goodnight Carson." Elizabeth echoed.

"Goodnight Elizabeth, Colonel." Carson stated, and with that he was finally gone leaving Elizabeth and John alone. For several seconds they just stared at each other in complete silence until Elizabeth could not take it anymore and she reached out to John and embraced him in a huge hug,

"Elizabeth…" John whispered returning the embrace. "I-"

"Oh John," Elizabeth interrupted, sighing into his shoulder as she sat herself down on the side of the bed and hugging John tighter. "I thought that I had lost you."

"Again," John stated with a smile.

"Again," Elizabeth agreed pulling out of the embrace and looking down at the bed.

"Elizabeth," John stated taking her hand in one of his and using the other to move her chine so he could look into her eyes. "I told you before and I'll tell you again, you will never loose me."

"But-" Elizabeth protested thinking of all the potentially horrible circumstances that could take him away from her forever.

"You'll never loose me," John continued. "Because I will always be here-" He stated pointing to her forehead, "-and here-" he continued, his voice softening as he pointed to her heart. "You'll never loose me."

"When did you become such a romantic?" Elizabeth asked, laughing through the tears that were spilling over her eyes.

"When I fell in love with you, I guess." John replied, throwing all caution to the wind and telling Elizabeth exactly how he felt.

"Oh-" Elizabeth choked out though a sob and she threw her arms around his neck again. "I've fallen in love with you too." She whispered into his ear.

John pushed her back to look at her and he saw that tears were falling out of her eyes. After he had wiped them off her cheeks he pulled her in for a passionate kiss. Several breathless moments later, they pulled apart and a horrible and soul-crushing thought struck her.

"Oh God John," Elizabeth began, her tears drying up out of fear. "What are we going to do now? Regulations state that-"

"They state that a leader cannot get involved with a subordinate officer, but Elizabeth, that is for the military. You are not military." John pointed out taking her hand to comfort her.

"But John," Elizabeth began. "You are and-"

"And besides," John continued. "I always thought that we were co-leaders of Atlantis."

"Un-officially yes," Elizabeth agreed. "But officially I am the sole person in charge of this expedition, and if the military ever found out, they might ask for your re-assignment."

"So what?" John asked, not thinking things through. "Do you want to wait until we are both free of this expedition? Come on Elizabeth, you're the smart on here. The Stargate program has been going on for ten- no eleven years now with no sign of stopping. Do you want to wait that long?"

"No." Elizabeth agreed shaking her head. "There is no way I could wait that long with out ever directly showing you how I felt about you."

"Good." John replied with a relieved sigh. "I mean, I would have- if you had asked me too, but now…after hearing you tell me- well let's just say it was going to be the hardest assignment that I have ever undertaken."

"But now what?" Elizabeth asked, her reasoning brining them both back to square one. "Now what are we going to do?"

"Now," John began choosing his words carefully. "We explore this relationship, see where it takes us… we'll worry about the military and regulations later."

"Are you sure you want to do this?" Elizabeth asked making sure that they were both on the same page.

"Elizabeth, I love you and I want to start a relationship with you….if you'll have me."

"Of course I'll have you." Elizabeth whispered placing a hand on his cheek. "I love you."

"And I love you Elizabeth."

The End

* * *

A/N- Yay! So I decded to forgo studying to finish this up (I thought that you loyal readers deserved that much). I know that a lot of this chapter was flashbacks but it was kinda important for the context of the story. So, The Link is over, but I think there might, and I stress, might be a sequel...but if there is a sequel it will not be out for a long time (I mean there is no concept at all, well, sorta...) If any of you have any ideas, feel free to put them in your reviews, who knows, maybe I will use one of them! Hope you enjoyed reading this, I know I enjoyed writing it and I hope that you all like this ending... Go and read some of the other Atlantis Fanfic for the time being and don't forget to REVIEW! Please! Thanks- Anjirika


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